From fafb6815569eda661ee8dbd81adcd9e9e7e72c19 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Sun, 8 Mar 2015 01:59:48 +0000 Subject: [PATCH] in progress, does NOT compile --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 323 ++ .../src/org/forester/archaeopteryx/MainFrame.java | 3546 ++++++++++---------- .../archaeopteryx/MainFrameApplication.java | 111 +- 3 files changed, 2152 insertions(+), 1828 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index d517e42..7426a4f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -3,6 +3,7 @@ package org.forester.archaeopteryx; import java.awt.BorderLayout; import java.awt.Container; +import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ComponentAdapter; @@ -18,6 +19,7 @@ import java.util.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; @@ -33,6 +35,8 @@ 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.webservices.PhylogeniesWebserviceClient; +import org.forester.archaeopteryx.webservices.WebservicesManager; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; @@ -135,7 +139,270 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private Phylogeny _species_tree; private JCheckBoxMenuItem _right_line_up_domains_cbmi; private JCheckBoxMenuItem _line_up_renderable_data_cbmi; + // file menu: + JMenuItem _open_item; + JMenuItem _open_url_item; + JMenuItem _save_item; + JMenuItem _save_all_item; + JMenuItem _close_item; + JMenuItem _exit_item; + JMenuItem _new_item; + JMenuItem _print_item; + JMenuItem _write_to_pdf_item; + JMenuItem _write_to_jpg_item; + JMenuItem _write_to_gif_item; + JMenuItem _write_to_tif_item; + JMenuItem _write_to_png_item; + JMenuItem _write_to_bmp_item; + JMenu _file_jmenu; + + + void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), + _mainpanel.getCurrentTreePanel().getHeight() ); + 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(); + } + + 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() == MainFrame.nhfilter ) { + exception = writeAsNewHampshire( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + exception = writeAsPhyloXml( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.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 ); + } + } + } + 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 ); + } + } + + 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() ); + } + } + + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); + } + _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); + _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); + if ( AptxUtil.canWriteFormat( "gif" ) ) { + _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); + } + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); + customizeJMenuItem( _save_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + customizeJMenuItem( _exit_item ); + _jmenubar.add( _file_jmenu ); + } + @Override public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); @@ -375,6 +642,59 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } updateOptions( getOptions() ); } + // + 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_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 == _write_to_png_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); + } + else if ( o == _print_item ) { + MainFrame.print( getCurrentTreePanel(), + getOptions(), + + this ); + + } + else if ( o == _save_item ) { + writeToFile( _mainpanel.getCurrentPhylogeny() ); + } + +// 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(); +// } + repaint(); } @@ -587,6 +907,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); _jmenubar = new JMenuBar(); if ( !getConfiguration().isHideControlPanelAndMenubar() ) { + buildFileMenu(); if ( !getConfiguration().isUseNativeUI() ) { _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); } @@ -946,12 +1267,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void customizeJMenuItem( final JMenuItem jmi ) { + if ( jmi != null ) { jmi.setFont( MainFrame.menu_font ); if ( !getConfiguration().isUseNativeUI() ) { jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); } jmi.addActionListener( this ); + } } void displayBasicInformation() { diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 85d2d68..9708688 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -80,308 +80,8 @@ import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; import org.forester.util.WindowsUtils; -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)"; - } -} - -public abstract class MainFrame extends JFrame implements ActionListener { - - /** - * Display the about box. - */ - static void about() { - final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2014 Christian M Zmasek\n" ); - about.append( "All Rights Reserved\n" ); - about.append( "License: GNU Lesser General Public License (LGPL)\n" ); - about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); - about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); - about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); - about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); - if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { - about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" ); - } - if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH ) - && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) { - about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " - + ForesterUtil.OS_VERSION + "]\n" ); - } - final Runtime rt = java.lang.Runtime.getRuntime(); - final long free_memory = rt.freeMemory() / 1000000; - final long total_memory = rt.totalMemory() / 1000000; - about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" ); - about.append( "[locale: " + Locale.getDefault() + "]\n" ); - about.append( "References:\n" ); - about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" ); - about.append( "For more information & download:\n" ); - about.append( Constants.APTX_WEB_SITE + "\n" ); - about.append( "Documentation:\n" ); - about.append( Constants.APTX_DOC_SITE + "\n" ); - about.append( "Comments: " + Constants.AUTHOR_EMAIL ); - JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); - } - - static void chooseNodeSize( final Options options, final Component parent ) { - final String s = ( String ) JOptionPane.showInputDialog( parent, - "Please enter the default size for node shapes.\n" - + "[current value: " - + options.getDefaultNodeShapeSize() + "]\n", - "Node Shape Size", - JOptionPane.QUESTION_MESSAGE, - null, - null, - options.getDefaultNodeShapeSize() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - final short size = ForesterUtil.roundToShort( m ); - if ( size >= 0.0 ) { - options.setDefaultNodeShapeSize( size ); - } - } - } - } - - static String createCurrentFontDesc( final TreeFontSet tree_font_set ) { - return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize(); - } - - static JMenu createMenu( final String title, final Configuration conf ) { - final JMenu jmenu = new JMenu( title ); - if ( !conf.isUseNativeUI() ) { - jmenu.setFont( MainFrame.menu_font ); - jmenu.setBackground( conf.getGuiMenuBackgroundColor() ); - jmenu.setForeground( conf.getGuiMenuTextColor() ); - } - return jmenu; - } - - static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) { - label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) ); - if ( !configuration.isUseNativeUI() ) { - label.setBackground( configuration.getGuiMenuBackgroundColor() ); - label.setForeground( configuration.getGuiMenuTextColor() ); - label.setOpaque( true ); - } - label.setSelected( false ); - label.setEnabled( false ); - return label; - } - - private static void cycleNodeDataReturn( final Options op, final Configuration conf ) { - switch ( op.getExtDescNodeDataToReturn() ) { - case UNKNOWN: - op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); - break; - case DOMAINS_ALL: - op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); - break; - case DOMAINS_COLLAPSED_PER_PROTEIN: - op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); - break; - case SEQ_ANNOTATIONS: - op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); - break; - case GO_TERM_IDS: - op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); - break; - case SEQUENCE_MOL_SEQ_FASTA: - if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null ) - && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL ) - && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) - && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS ) - && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) - && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) { - op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); - } - else { - op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); - } - break; - default: - op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); - } - } - - static void cycleNodeFill( final Options op ) { - switch ( op.getDefaultNodeFill() ) { - case GRADIENT: - op.setDefaultNodeFill( NodeFill.SOLID ); - break; - case NONE: - op.setDefaultNodeFill( NodeFill.GRADIENT ); - break; - case SOLID: - op.setDefaultNodeFill( NodeFill.NONE ); - break; - default: - throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); - } - } - - static void cycleNodeShape( final Options op ) { - switch ( op.getDefaultNodeShape() ) { - case CIRCLE: - op.setDefaultNodeShape( NodeShape.RECTANGLE ); - break; - case RECTANGLE: - op.setDefaultNodeShape( NodeShape.CIRCLE ); - break; - default: - throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); - } - } - - static void cycleOverview( final Options op, final TreePanel tree_panel ) { - switch ( op.getOvPlacement() ) { - case LOWER_LEFT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - break; - case LOWER_RIGHT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); - break; - case UPPER_LEFT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); - break; - case UPPER_RIGHT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); - break; - default: - throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); - } - if ( tree_panel != null ) { - tree_panel.updateOvSettings(); - } - } - - static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { - mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" ); - } - else { - mi.setText( "Cycle Node Return Data..." ); - } - } - - static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { - mi.setText( "Cycle Node Shape Fill Type... (current: " - + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); - } - else { - mi.setText( "Cycle Node Shape Fill Type..." ); - } - } - - static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { - mi.setText( "Cycle Node Shape Fill Type... (current: " - + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); - } - else { - mi.setText( "Cycle Node Shape Fill Type..." ); - } - } - - static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { - mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); - } - else { - mi.setText( "Cycle Overview Placement..." ); - } - } - - static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { - if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { - mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() - + ")" ); - } - else { - mi.setText( "Select Color Scheme..." ); - } - } - - static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) { - mi.setText( "Select Default Font... (current: " + font_desc + ")" ); - } - - static void 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 setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) { - if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { - mi.setEnabled( true ); - } - else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { - mi.setEnabled( true ); - } - else { - mi.setEnabled( false ); - } - mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); - } - - static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { - mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); - } +public abstract class MainFrame extends JFrame implements ActionListener { - static void updateScreenTextAntialias( final List treepanels ) { - for( final TreePanel tree_panel : treepanels ) { - tree_panel.setTextAntialias(); - } - } final static NHFilter nhfilter = new NHFilter(); final static NHXFilter nhxfilter = new NHXFilter(); final static XMLFilter xmlfilter = new XMLFilter(); @@ -557,7 +257,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _curved_type_cbmi; JCheckBoxMenuItem _convex_type_cbmi; JCheckBoxMenuItem _euro_type_cbmi; - JCheckBoxMenuItem _rounded_type_cbmi; ; + JCheckBoxMenuItem _rounded_type_cbmi; JCheckBoxMenuItem _unrooted_type_cbmi; JCheckBoxMenuItem _circular_type_cbmi; // view as text menu: @@ -582,7 +282,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; - final LinkedList _textframes = new LinkedList(); + final LinkedList _textframes = new LinkedList(); ; Configuration _configuration; Options _options; private Phylogeny _species_tree; @@ -779,1674 +479,2078 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_default_node_shapes_for_marked_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _non_lined_up_cladograms_rbmi ) { - updateOptions( getOptions() ); - showWhole(); + else if ( o == _non_lined_up_cladograms_rbmi ) { + updateOptions( getOptions() ); + showWhole(); + } + else if ( o == _uniform_cladograms_rbmi ) { + updateOptions( getOptions() ); + showWhole(); + } + else if ( o == _ext_node_dependent_cladogram_rbmi ) { + updateOptions( getOptions() ); + showWhole(); + } + else if ( o == _search_case_senstive_cbmi ) { + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _search_whole_words_only_cbmi ) { + if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { + _search_with_regex_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _inverse_search_result_cbmi ) { + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _search_with_regex_cbmi ) { + if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_whole_words_only_cbmi.setSelected( false ); + } + if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_case_senstive_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + } + else if ( o == _show_scale_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_confidence_stddev_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { + if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { + if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _label_direction_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_overview_cbmi ) { + updateOptions( getOptions() ); + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().updateOvSizes(); + } + } + else if ( o == _line_up_renderable_data_cbmi ) { + if ( !_line_up_renderable_data_cbmi.isSelected() ) { + _right_line_up_domains_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _right_line_up_domains_cbmi ) { + if ( _right_line_up_domains_cbmi.isSelected() ) { + _line_up_renderable_data_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } + else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) + || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi ) + || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { + typeChanged( o ); + } + else if ( o == _about_item ) { + about(); + } + else if ( o == _help_item ) { + try { + AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _website_item ) { + try { + AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_website_item ) { + try { + AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _aptx_ref_item ) { + try { + AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _phyloxml_ref_item ) { + try { + AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _write_to_pdf_item ) { + writeToPdf( _mainpanel.getCurrentPhylogeny() ); + } + else if ( o == _save_all_item ) { + writeAllToFile(); + } + else if ( o == _write_to_jpg_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); + } + 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( getCurrentTreePanel(), + getOptions(), + + this ); + } + else if ( o == _save_item ) { + writeToFile( _mainpanel.getCurrentPhylogeny() ); + } + else if ( o == _write_to_png_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); + } + 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 ( _load_phylogeny_from_webservice_menu_items != null ) { + for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { + if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { + readPhylogeniesFromWebservice( i ); + } + } + } + } + _contentpane.repaint(); + } + + public Configuration getConfiguration() { + return _configuration; + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + + public MainPanel getMainPanel() { + return _mainpanel; + } + + public Options getOptions() { + return _options; + } + + public ProcessPool getProcessPool() { + return _process_pool; + } + + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + public void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + + public void updateProcessMenu() { + // In general Swing is not thread safe. + // See "Swing's Threading Policy". + SwingUtilities.invokeLater( new Runnable() { + + @Override + public void run() { + doUpdateProcessMenu(); + } + } ); + } + + void activateSaveAllIfNeeded() { + if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) { + _save_all_item.setEnabled( true ); + } + else { + _save_all_item.setEnabled( false ); } - else if ( o == _uniform_cladograms_rbmi ) { - updateOptions( getOptions() ); - showWhole(); + } + + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); } - else if ( o == _ext_node_dependent_cladogram_rbmi ) { - updateOptions( getOptions() ); - showWhole(); + _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..." ) ); } - else if ( o == _search_case_senstive_cbmi ) { - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); } - else if ( o == _search_whole_words_only_cbmi ) { - if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { - _search_with_regex_cbmi.setSelected( false ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); + customizeJMenuItem( _save_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + customizeJMenuItem( _exit_item ); + _jmenubar.add( _file_jmenu ); + } + + void buildFontSizeMenu() { + _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() ); + _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) ); + _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) ); + _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) ); + _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) ); + _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) ); + customizeJMenuItem( _super_tiny_fonts_item ); + customizeJMenuItem( _tiny_fonts_item ); + customizeJMenuItem( _small_fonts_item ); + customizeJMenuItem( _medium_fonts_item ); + customizeJMenuItem( _large_fonts_item ); + _jmenubar.add( _font_size_menu ); + } + + void buildHelpMenu() { + _help_jmenu = createMenu( "Help", getConfiguration() ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); + _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); + _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... + _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); + _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); + _help_jmenu.addSeparator(); + _help_jmenu.add( _about_item = new JMenuItem( "About" ) ); + customizeJMenuItem( _help_item ); + customizeJMenuItem( _website_item ); + customizeJMenuItem( _phyloxml_website_item ); + customizeJMenuItem( _aptx_ref_item ); + customizeJMenuItem( _phyloxml_ref_item ); + customizeJMenuItem( _about_item ); + _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP ); + _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP ); + _jmenubar.add( _help_jmenu ); + } + + void buildTypeMenu() { + _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() ); + _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); + _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) ); + _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) ); + _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) ); + _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) ); + _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) ); + _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) ); + _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) ); + customizeCheckBoxMenuItem( _rectangular_type_cbmi, false ); + customizeCheckBoxMenuItem( _triangular_type_cbmi, false ); + customizeCheckBoxMenuItem( _euro_type_cbmi, false ); + customizeCheckBoxMenuItem( _rounded_type_cbmi, false ); + customizeCheckBoxMenuItem( _curved_type_cbmi, false ); + customizeCheckBoxMenuItem( _convex_type_cbmi, false ); + customizeCheckBoxMenuItem( _unrooted_type_cbmi, false ); + customizeCheckBoxMenuItem( _circular_type_cbmi, false ); + _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); + _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); + initializeTypeMenu( getOptions() ); + _jmenubar.add( _type_menu ); + } + + void buildViewMenu() { + _view_jmenu = createMenu( "View", getConfiguration() ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) ); + _view_jmenu.addSeparator(); + _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); + _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); + _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); + customizeJMenuItem( _display_basic_information_item ); + customizeJMenuItem( _view_as_NH_item ); + customizeJMenuItem( _view_as_XML_item ); + customizeJMenuItem( _view_as_nexus_item ); + _jmenubar.add( _view_jmenu ); + } + + void checkTextFrames() { + if ( _textframes.size() > 5 ) { + try { + if ( _textframes.getFirst() != null ) { + _textframes.getFirst().removeMe(); + } + else { + _textframes.removeFirst(); + } + } + catch ( final NoSuchElementException e ) { + // Ignore. } - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); - } - else if ( o == _inverse_search_result_cbmi ) { - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); } - else if ( o == _search_with_regex_cbmi ) { - if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { - _search_whole_words_only_cbmi.setSelected( false ); + } + + 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; + } } - if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { - _search_case_senstive_cbmi.setSelected( true ); + else { + success = false; + } + if ( success && ( f > 0.0 ) ) { + getOptions().setPrintLineWidth( f ); } - updateOptions( getOptions() ); - getMainPanel().getControlPanel().search0(); - getMainPanel().getControlPanel().search1(); } - else if ( o == _show_scale_cbmi ) { - updateOptions( getOptions() ); + } + + 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 ); + } } - else if ( o == _color_by_taxonomic_group_cbmi ) { - updateOptions( getOptions() ); + } + + void close() { + removeAllTextFrames(); + if ( _mainpanel != null ) { + _mainpanel.terminate(); } - else if ( o == _show_confidence_stddev_cbmi ) { - updateOptions( getOptions() ); + if ( _contentpane != null ) { + _contentpane.removeAll(); } - else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { - if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { - _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); + setVisible( false ); + dispose(); + } + + void colorRank() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + final String[] ranks = AptxUtil.getAllPossibleRanks(); + final String rank = ( String ) JOptionPane + .showInputDialog( this, + "What rank should the colorization be based on", + "Rank Selection", + JOptionPane.QUESTION_MESSAGE, + null, + ranks, + null ); + if ( !ForesterUtil.isEmpty( rank ) ) { + _mainpanel.getCurrentTreePanel().colorRank( rank ); } - updateOptions( getOptions() ); } - else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { - if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { - _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); - } - updateOptions( getOptions() ); + } + + void confColor() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().confColor(); } - else if ( o == _label_direction_cbmi ) { - updateOptions( getOptions() ); + } + + void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { + if ( item != null ) { + item.setFont( MainFrame.menu_font ); + if ( !getConfiguration().isUseNativeUI() ) { + item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + item.setForeground( getConfiguration().getGuiMenuTextColor() ); + } + item.setSelected( is_selected ); + item.addActionListener( this ); } - else if ( o == _show_overview_cbmi ) { - updateOptions( getOptions() ); - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().updateOvSizes(); + } + + JMenuItem customizeJMenuItem( final JMenuItem jmi ) { + if ( jmi != null ) { + jmi.setFont( MainFrame.menu_font ); + if ( !getConfiguration().isUseNativeUI() ) { + jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); } + jmi.addActionListener( this ); } - else if ( o == _line_up_renderable_data_cbmi ) { - if ( !_line_up_renderable_data_cbmi.isSelected() ) { - _right_line_up_domains_cbmi.setSelected( false ); + return jmi; + } + + void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { + if ( item != null ) { + item.setFont( MainFrame.menu_font ); + if ( !getConfiguration().isUseNativeUI() ) { + item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + item.setForeground( getConfiguration().getGuiMenuTextColor() ); } - updateOptions( getOptions() ); + item.setSelected( is_selected ); + item.addActionListener( this ); } - else if ( o == _right_line_up_domains_cbmi ) { - if ( _right_line_up_domains_cbmi.isSelected() ) { - _line_up_renderable_data_cbmi.setSelected( true ); + } + + void displayBasicInformation( final File treefile ) { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "Basic Information"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - updateOptions( getOptions() ); + showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title ); } - else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi ) - || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi ) - || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) { - typeChanged( o ); + } + + void exceptionOccuredDuringOpenFile( final Exception e ) { + try { + _mainpanel.getCurrentTreePanel().setArrowCursor(); } - else if ( o == _about_item ) { - about(); + catch ( final Exception ex ) { + // Do nothing. } - else if ( o == _help_item ) { - try { - AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } + JOptionPane.showMessageDialog( this, + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), + "Error during File|Open", + JOptionPane.ERROR_MESSAGE ); + } + + void exceptionOccuredDuringSaveAs( final Exception e ) { + try { + _mainpanel.getCurrentTreePanel().setArrowCursor(); } - else if ( o == _website_item ) { - try { - AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } + catch ( final Exception ex ) { + // Do nothing. } - else if ( o == _phyloxml_website_item ) { - try { - AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } + JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); + } + + void executeGSDI() { + if ( !isOKforSDI( false, true ) ) { + return; } - else if ( o == _aptx_ref_item ) { - try { - AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not rooted.", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; } - else if ( o == _phyloxml_ref_item ) { - try { - AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet ); - } - catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); - } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDI gsdi = null; + final Phylogeny species_tree = getSpeciesTree().copy(); + try { + gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); } - else if ( o == _write_to_pdf_item ) { - writeToPdf( _mainpanel.getCurrentPhylogeny() ); + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDI", + JOptionPane.ERROR_MESSAGE ); + return; } - else if ( o == _save_item ) { - writeToFile( _mainpanel.getCurrentPhylogeny() ); - // If subtree currently displayed, save it, instead of complete - // tree. + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; } - else if ( o == _write_to_png_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); + gene_tree.setRerootable( false ); + gene_tree.clearHashIdToNodeMap(); + gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); } - else if ( o == _graphics_export_visible_only_cbmi ) { - updateOptions( getOptions() ); + else { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } - else if ( o == _antialias_print_cbmi ) { - updateOptions( getOptions() ); + } + + void executeGSDIR() { + if ( !isOKforSDI( false, false ) ) { + return; } - else if ( o == _print_black_and_white_cbmi ) { - updateOptions( getOptions() ); + final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); + if ( ( p > 0 ) + && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; } - else if ( o == _print_using_actual_size_cbmi ) { - updateOptions( getOptions() ); + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDIR gsdir = null; + final Phylogeny species_tree = getSpeciesTree().copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); } - else if ( o == _graphics_export_using_actual_size_cbmi ) { - updateOptions( getOptions() ); + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDIR", + JOptionPane.ERROR_MESSAGE ); + return; } - else if ( o == _print_size_mi ) { - choosePrintSize(); + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; } - else if ( o == _choose_pdf_width_mi ) { - choosePdfWidth(); + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); + result_gene_tree.setRerootable( false ); + result_gene_tree.clearHashIdToNodeMap(); + result_gene_tree.recalculateNumberOfExternalDescendants( true ); + PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { - if ( _load_phylogeny_from_webservice_menu_items != null ) { - for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { - if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { - readPhylogeniesFromWebservice( i ); - } - } - } + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } - _contentpane.repaint(); } - void activateSaveAllIfNeeded() { - if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) { - _save_all_item.setEnabled( true ); + boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { + if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { + JOptionPane.showMessageDialog( this, + "Gene tree and species tree have no species in common.", + "Error during SDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree.getNumberOfExternalNodes() < 2 ) { + JOptionPane.showMessageDialog( this, + "Gene tree and species tree have only one species in common.", + "Error during SDI", + JOptionPane.ERROR_MESSAGE ); + return false; } else { - _save_all_item.setEnabled( false ); + return true; } } - private void annotateSequences() { - if ( getCurrentTreePanel() != null ) { - List nodes = null; - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) - || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + ControlPanel getControlPanel() { + return getMainPanel().getControlPanel(); + } + + File getCurrentDir() { + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( ForesterUtil.isWindows() ) { + try { + _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); + } + catch ( final Exception e ) { + _current_dir = null; + } } - if ( ( nodes == null ) || nodes.isEmpty() ) { - JOptionPane - .showMessageDialog( this, - "Need to select nodes, either via direct selection or via the \"Search\" function", - "No nodes selected for annotation", - JOptionPane.ERROR_MESSAGE ); - return; + } + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( System.getProperty( "user.home" ) != null ) { + _current_dir = new File( System.getProperty( "user.home" ) ); } - final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final JTextField ref_field = new JTextField( 10 ); - final JTextField desc_filed = new JTextField( 20 ); - ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" - : getPreviousNodeAnnotationReference() ); - final JPanel my_panel = new JPanel(); - my_panel.add( new JLabel( "Reference " ) ); - my_panel.add( ref_field ); - my_panel.add( Box.createHorizontalStrut( 15 ) ); - my_panel.add( new JLabel( "Description " ) ); - my_panel.add( desc_filed ); - final int result = JOptionPane.showConfirmDialog( null, - my_panel, - "Enter the sequence annotation(s) for the " - + nodes.size() + " selected nodes", - JOptionPane.OK_CANCEL_OPTION ); - if ( result == JOptionPane.OK_OPTION ) { - String ref = ref_field.getText(); - String desc = desc_filed.getText(); - if ( !ForesterUtil.isEmpty( ref ) ) { - ref = ref.trim(); - ref = ref.replaceAll( "\\s+", " " ); - if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) ) - || ( ref.length() < 3 ) ) { - JOptionPane.showMessageDialog( this, - "Reference needs to be in the form of \"GO:1234567\"", - "Illegal Format for Annotation Reference", - JOptionPane.ERROR_MESSAGE ); - return; - } - } - if ( ref != null ) { - setPreviousNodeAnnotationReference( ref ); - } - if ( desc != null ) { - desc = desc.trim(); - desc = desc.replaceAll( "\\s+", " " ); - } - if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { - for( final PhylogenyNode n : nodes ) { - ForesterUtil.ensurePresenceOfSequence( n ); - final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() - : new Annotation( ref ); - if ( !ForesterUtil.isEmpty( desc ) ) { - ann.setDesc( desc ); - } - n.getNodeData().getSequence().addAnnotation( ann ); - } - } - getMainPanel().getControlPanel().showAnnotations(); - } + else if ( System.getProperty( "user.dir" ) != null ) { + _current_dir = new File( System.getProperty( "user.dir" ) ); } } + return _current_dir; } - // void buildFileMenu() { - // _file_jmenu = createMenu( "File", getConfiguration() ); - // _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); - // customizeJMenuItem( _exit_item ); - // _jmenubar.add( _file_jmenu ); - // } - void buildFileMenu() { - _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); - _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( _exit_item = new JMenuItem( "Exit" ) ); - customizeJMenuItem( _save_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 ); + TreePanel getCurrentTreePanel() { + return getMainPanel().getCurrentTreePanel(); } - void buildFontSizeMenu() { - _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() ); - _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) ); - _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) ); - _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) ); - _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) ); - _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) ); - customizeJMenuItem( _super_tiny_fonts_item ); - customizeJMenuItem( _tiny_fonts_item ); - customizeJMenuItem( _small_fonts_item ); - customizeJMenuItem( _medium_fonts_item ); - customizeJMenuItem( _large_fonts_item ); - _jmenubar.add( _font_size_menu ); + JMenu getHelpMenu() { + return _help_jmenu; } - void buildHelpMenu() { - _help_jmenu = createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); - _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this... - _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); - _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) ); - _help_jmenu.addSeparator(); - _help_jmenu.add( _about_item = new JMenuItem( "About" ) ); - customizeJMenuItem( _help_item ); - customizeJMenuItem( _website_item ); - customizeJMenuItem( _phyloxml_website_item ); - customizeJMenuItem( _aptx_ref_item ); - customizeJMenuItem( _phyloxml_ref_item ); - customizeJMenuItem( _about_item ); - _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP ); - _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP ); - _jmenubar.add( _help_jmenu ); + JCheckBoxMenuItem getlabelDirectionCbmi() { + return _label_direction_cbmi; } - void buildTypeMenu() { - _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() ); - _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); - _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) ); - _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) ); - _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) ); - _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) ); - _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) ); - customizeCheckBoxMenuItem( _rectangular_type_cbmi, false ); - customizeCheckBoxMenuItem( _triangular_type_cbmi, false ); - customizeCheckBoxMenuItem( _euro_type_cbmi, false ); - customizeCheckBoxMenuItem( _rounded_type_cbmi, false ); - customizeCheckBoxMenuItem( _curved_type_cbmi, false ); - customizeCheckBoxMenuItem( _convex_type_cbmi, false ); - customizeCheckBoxMenuItem( _unrooted_type_cbmi, false ); - customizeCheckBoxMenuItem( _circular_type_cbmi, false ); - _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); - _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); - initializeTypeMenu( getOptions() ); - _jmenubar.add( _type_menu ); + JMenuBar getMenuBarOfMainFrame() { + return _jmenubar; } - void buildViewMenu() { - _view_jmenu = createMenu( "View", getConfiguration() ); - _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) ); - _view_jmenu.addSeparator(); - _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); - _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); - _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); - customizeJMenuItem( _display_basic_information_item ); - customizeJMenuItem( _view_as_NH_item ); - customizeJMenuItem( _view_as_XML_item ); - customizeJMenuItem( _view_as_nexus_item ); - _jmenubar.add( _view_jmenu ); + final Phylogeny getSpeciesTree() { + return _species_tree; + } + + void initializeTypeMenu( final Options options ) { + setTypeMenuToAllUnselected(); + switch ( options.getPhylogenyGraphicsType() ) { + case CONVEX: + _convex_type_cbmi.setSelected( true ); + break; + case CURVED: + _curved_type_cbmi.setSelected( true ); + break; + case EURO_STYLE: + _euro_type_cbmi.setSelected( true ); + break; + case ROUNDED: + _rounded_type_cbmi.setSelected( true ); + break; + case TRIANGULAR: + _triangular_type_cbmi.setSelected( true ); + break; + case UNROOTED: + _unrooted_type_cbmi.setSelected( true ); + break; + case CIRCULAR: + _circular_type_cbmi.setSelected( true ); + break; + default: + _rectangular_type_cbmi.setSelected( true ); + break; + } + } + + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Species tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else { + return true; + } } - void checkTextFrames() { - if ( _textframes.size() > 5 ) { - try { - if ( _textframes.getFirst() != null ) { - _textframes.getFirst().removeMe(); - } - else { - _textframes.removeFirst(); - } - } - catch ( final NoSuchElementException e ) { - // Ignore. + boolean isSubtreeDisplayed() { + if ( getCurrentTreePanel() != null ) { + if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { + JOptionPane + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); + return true; } } + return false; } - private void chooseFont() { - final FontChooser fc = new FontChooser(); - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); - fc.showDialog( this, "Select the Base Font" ); - getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); + void midpointRoot() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().midpointRoot(); + } } - private void chooseMinimalConfidence() { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please enter the minimum for confidence values to be displayed.\n" - + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } + void printPhylogenyToPdf( final String file_name ) { + if ( !getOptions().isPrintUsingActualSize() ) { + getCurrentTreePanel() + .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() ); + 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 { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - getOptions().setMinConfidenceValue( m ); + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions() + .getPrintSizeX(), getOptions().getPrintSizeY() ); } } - } - - 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; - } + 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 { - success = false; - } - if ( success && ( f > 0.0 ) ) { - getOptions().setPrintLineWidth( f ); + 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(); + } } - 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 ); + void readPhylogeniesFromWebservice( final int i ) { + final UrlTreeReader reader = new UrlTreeReader( this, i ); + new Thread( reader ).start(); + } + + void removeAllTextFrames() { + for( final TextFrame tf : _textframes ) { + if ( tf != null ) { + tf.close(); } } + _textframes.clear(); } - void close() { - removeAllTextFrames(); - if ( _mainpanel != null ) { - _mainpanel.terminate(); - } - if ( _contentpane != null ) { - _contentpane.removeAll(); - } - setVisible( false ); - dispose(); + void resetSearch() { + getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); + getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); } - void colorRank() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - final String[] ranks = AptxUtil.getAllPossibleRanks(); - final String rank = ( String ) JOptionPane - .showInputDialog( this, - "What rank should the colorization be based on", - "Rank Selection", - JOptionPane.QUESTION_MESSAGE, - null, - ranks, - null ); - if ( !ForesterUtil.isEmpty( rank ) ) { - _mainpanel.getCurrentTreePanel().colorRank( rank ); - } + void setConfiguration( final Configuration configuration ) { + _configuration = configuration; + } + + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + + void setInferenceManager( final InferenceManager i ) { + _inference_manager = i; + } + + void setOptions( final Options options ) { + _options = options; + } + + void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { + setTypeMenuToAllUnselected(); + switch ( type ) { + case CIRCULAR: + _circular_type_cbmi.setSelected( true ); + break; + case CONVEX: + _convex_type_cbmi.setSelected( true ); + break; + case CURVED: + _curved_type_cbmi.setSelected( true ); + break; + case EURO_STYLE: + _euro_type_cbmi.setSelected( true ); + break; + case ROUNDED: + _rounded_type_cbmi.setSelected( true ); + break; + case RECTANGULAR: + _rectangular_type_cbmi.setSelected( true ); + break; + case TRIANGULAR: + _triangular_type_cbmi.setSelected( true ); + break; + case UNROOTED: + _unrooted_type_cbmi.setSelected( true ); + break; + default: + throw new IllegalArgumentException( "unknown type: " + type ); } } - void confColor() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().confColor(); - } + final void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; } - void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { - if ( item != null ) { - item.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - item.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - item.setSelected( is_selected ); - item.addActionListener( this ); - } + void setTypeMenuToAllUnselected() { + _convex_type_cbmi.setSelected( false ); + _curved_type_cbmi.setSelected( false ); + _euro_type_cbmi.setSelected( false ); + _rounded_type_cbmi.setSelected( false ); + _triangular_type_cbmi.setSelected( false ); + _rectangular_type_cbmi.setSelected( false ); + _unrooted_type_cbmi.setSelected( false ); + _circular_type_cbmi.setSelected( false ); } - JMenuItem customizeJMenuItem( final JMenuItem jmi ) { - if ( jmi != null ) { - jmi.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - jmi.addActionListener( this ); - } - return jmi; + void switchColors() { + final TreeColorSet colorset = _mainpanel.getTreeColorSet(); + final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); + csc.setVisible( true ); } - void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { - if ( item != null ) { - item.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - item.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - item.setSelected( is_selected ); - item.addActionListener( this ); + void taxColor() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().taxColor(); } } - private void deleteSelectedNodes( final boolean delete ) { - final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); - if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { - return; - } - final List nodes = new ArrayList(); - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); - for( final PhylogenyNode n : all_selected_nodes ) { - if ( n.isExternal() ) { - nodes.add( n ); - } + void typeChanged( final Object o ) { + updateTypeCheckboxes( getOptions(), o ); + updateOptions( getOptions() ); + if ( getCurrentTreePanel() != null ) { + final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType(); + final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType(); + if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) + || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) + || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) + || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) { + getCurrentTreePanel().getControlPanel().showWhole(); } - } - String function = "Retain"; - if ( delete ) { - function = "Delete"; - } - if ( ( nodes == null ) || nodes.isEmpty() ) { - JOptionPane - .showMessageDialog( this, - "Need to select external nodes, either via direct selection or via the \"Search\" function", - "No external nodes selected to " + function.toLowerCase(), - JOptionPane.ERROR_MESSAGE ); - return; - } - final int todo = nodes.size(); - final int ext = phy.getNumberOfExternalNodes(); - int res = todo; - if ( delete ) { - res = ext - todo; - } - if ( res < 1 ) { - JOptionPane.showMessageDialog( this, - "Cannot delete all nodes", - "Attempt to delete all nodes ", - JOptionPane.ERROR_MESSAGE ); - return; - } - final int result = JOptionPane.showConfirmDialog( null, function + " " + todo - + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res - + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); - if ( result == JOptionPane.OK_OPTION ) { - if ( !delete ) { - final List to_delete = new ArrayList(); - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !nodes.contains( n ) ) { - to_delete.add( n ); - } - } - for( final PhylogenyNode n : to_delete ) { - phy.deleteSubtree( n, true ); - } + if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true ); } else { - for( final PhylogenyNode n : nodes ) { - phy.deleteSubtree( n, true ); - } - } - resetSearch(); - getCurrentTreePanel().setNodeInPreorderToNull(); - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().setEdited( true ); - repaint(); - } - } - - void displayBasicInformation( final File treefile ) { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "Basic Information"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; - } - showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title ); - } - } - - private void doUpdateProcessMenu() { - if ( _process_pool.size() > 0 ) { - if ( _process_menu == null ) { - _process_menu = createMenu( "", getConfiguration() ); - _process_menu.setForeground( Color.RED ); - } - _process_menu.removeAll(); - final String text = "processes running: " + _process_pool.size(); - _process_menu.setText( text ); - _jmenubar.add( _process_menu ); - for( int i = 0; i < _process_pool.size(); ++i ) { - final ProcessRunning p = _process_pool.getProcessByIndex( i ); - _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false ); } - } - else { - if ( _process_menu != null ) { - _process_menu.removeAll(); - _jmenubar.remove( _process_menu ); + getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() ); + updateScreenTextAntialias( getMainPanel().getTreePanels() ); + if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) { + if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false ); + } + else { + getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true ); + } } } - _jmenubar.validate(); - _jmenubar.repaint(); - repaint(); - } - - void exceptionOccuredDuringOpenFile( final Exception e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - JOptionPane.showMessageDialog( this, - ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Error during File|Open", - JOptionPane.ERROR_MESSAGE ); - } - - void exceptionOccuredDuringSaveAs( final Exception e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); } - void executeGSDI() { - if ( !isOKforSDI( false, true ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not rooted.", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDI gsdi = null; - final Phylogeny species_tree = getSpeciesTree().copy(); - try { - gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); - } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; - } - gene_tree.setRerootable( false ); - gene_tree.clearHashIdToNodeMap(); - gene_tree.recalculateNumberOfExternalDescendants( true ); - _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); - getMainPanel().getControlPanel().setShowEvents( true ); - showWhole(); - final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); - _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); - showWhole(); - _mainpanel.getTabbedPane().setSelectedIndex( selected ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); - if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { - JOptionPane.showMessageDialog( this, - "Duplications: " + gsdi.getDuplicationsSum() + "\n" - + "Potential duplications: " - + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" - + "Speciations: " + gsdi.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.WARNING_MESSAGE ); + void updateOptions( final Options options ) { + options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); + options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) + && _background_gradient_cbmi.isSelected() ); + options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); + options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) + && _show_annotation_ref_source.isSelected() ); + options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) + && _abbreviate_scientific_names.isSelected() ); + options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) + && _color_labels_same_as_parent_branch.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); + if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } - else { - JOptionPane.showMessageDialog( this, - "Duplications: " + gsdi.getDuplicationsSum() + "\n" - + "Potential duplications: " - + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" - + "Speciations: " + gsdi.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); } - } - - void executeGSDIR() { - if ( !isOKforSDI( false, false ) ) { - return; + else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) { + options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); } - final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); - if ( ( p > 0 ) - && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return; + options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) + && _search_case_senstive_cbmi.isSelected() ); + if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { + options.setShowScale( _show_scale_cbmi.isSelected() ); } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDIR gsdir = null; - final Phylogeny species_tree = getSpeciesTree().copy(); - try { - gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); + if ( _label_direction_cbmi != null ) { + if ( _label_direction_cbmi.isSelected() ) { + options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); + } + else { + options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); + } } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDIR", - JOptionPane.ERROR_MESSAGE ); - return; + options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); + options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) + && _show_confidence_stddev_cbmi.isSelected() ); + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; + options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) + && ( _print_using_actual_size_cbmi.isSelected() ) ); + options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) + && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); + options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); + if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) + && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); } - final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); - result_gene_tree.setRerootable( false ); - result_gene_tree.clearHashIdToNodeMap(); - result_gene_tree.recalculateNumberOfExternalDescendants( true ); - PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); - _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); - getMainPanel().getControlPanel().setShowEvents( true ); - showWhole(); - final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); - _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); - showWhole(); - _mainpanel.getTabbedPane().setSelectedIndex( selected ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); - if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { - JOptionPane.showMessageDialog( this, - "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" - + "Speciations: " + gsdir.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.WARNING_MESSAGE ); + else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) + && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); } else { - JOptionPane.showMessageDialog( this, - "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" - + "Speciations: " + gsdir.getSpeciationsSum() + "\n" - + "Stripped gene tree nodes: " - + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" - + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" - + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); } - } - - boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { - if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { - JOptionPane.showMessageDialog( this, - "Gene tree and species tree have no species in common.", - "Error during SDI", - JOptionPane.ERROR_MESSAGE ); - return false; + options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) + && _print_black_and_white_cbmi.isSelected() ); + options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) + && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); + if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } - else if ( gene_tree.getNumberOfExternalNodes() < 2 ) { - JOptionPane.showMessageDialog( this, - "Gene tree and species tree have only one species in common.", - "Error during SDI", - JOptionPane.ERROR_MESSAGE ); - return false; + else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } - else { - return true; + else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } - } - - public Configuration getConfiguration() { - return _configuration; - } - - ControlPanel getControlPanel() { - return getMainPanel().getControlPanel(); - } - - File getCurrentDir() { - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( ForesterUtil.isWindows() ) { - try { - _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); - } - catch ( final Exception e ) { - _current_dir = null; - } - } + else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( System.getProperty( "user.home" ) != null ) { - _current_dir = new File( System.getProperty( "user.home" ) ); + options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) + && _replace_underscores_cbmi.isSelected() ); + options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) + && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); + options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) + && _search_whole_words_only_cbmi.isSelected() ); + options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); + options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) + && _inverse_search_result_cbmi.isSelected() ); + if ( _graphics_export_visible_only_cbmi != null ) { + options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); + if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) { + _graphics_export_using_actual_size_cbmi.setSelected( true ); + _graphics_export_using_actual_size_cbmi.setEnabled( false ); } - else if ( System.getProperty( "user.dir" ) != null ) { - _current_dir = new File( System.getProperty( "user.dir" ) ); + else { + _graphics_export_using_actual_size_cbmi.setEnabled( true ); } } - return _current_dir; - } - - /** - * This method returns the current external node data which - * has been selected by the user by clicking the "Return ..." - * menu item. This method is expected to be called from Javascript or - * something like it. - * - * @return current external node data as String - */ - public String getCurrentExternalNodesDataBuffer() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); - } - - public int getCurrentExternalNodesDataBufferChangeCounter() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); - } - - public int getCurrentExternalNodesDataBufferLength() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); - } - - TreePanel getCurrentTreePanel() { - return getMainPanel().getCurrentTreePanel(); - } - - JMenu getHelpMenu() { - return _help_jmenu; - } - - public InferenceManager getInferenceManager() { - return _inference_manager; + if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + } + else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + } + else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + } + else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + } + else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + } + else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + } + else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { + options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + } + if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { + options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { + options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + } } - JCheckBoxMenuItem getlabelDirectionCbmi() { - return _label_direction_cbmi; + void updateTypeCheckboxes( final Options options, final Object o ) { + setTypeMenuToAllUnselected(); + ( ( JCheckBoxMenuItem ) o ).setSelected( true ); } - public MainPanel getMainPanel() { - return _mainpanel; + void viewAsNexus() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), + title ); + } } - JMenuBar getMenuBarOfMainFrame() { - return _jmenubar; + void viewAsNH() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() + .getNhConversionSupportValueStyle() ), + title ); + } } - public Options getOptions() { - return _options; + void viewAsXML() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); + } } - private String getPreviousNodeAnnotationReference() { - return _previous_node_annotation_ref; + 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; } - public ProcessPool getProcessPool() { - return _process_pool; + 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; } - final Phylogeny getSpeciesTree() { - return _species_tree; + 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; } - void initializeTypeMenu( final Options options ) { - setTypeMenuToAllUnselected(); - switch ( options.getPhylogenyGraphicsType() ) { - case CONVEX: - _convex_type_cbmi.setSelected( true ); - break; - case CURVED: - _curved_type_cbmi.setSelected( true ); - break; - case EURO_STYLE: - _euro_type_cbmi.setSelected( true ); - break; - case ROUNDED: - _rounded_type_cbmi.setSelected( true ); - break; - case TRIANGULAR: - _triangular_type_cbmi.setSelected( true ); - break; - case UNROOTED: - _unrooted_type_cbmi.setSelected( true ); - break; - case CIRCULAR: - _circular_type_cbmi.setSelected( true ); - break; - default: - _rectangular_type_cbmi.setSelected( true ); - break; + void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), + _mainpanel.getCurrentTreePanel().getHeight() ); + 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(); } - boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { - if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { - return false; - } - else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { - JOptionPane.showMessageDialog( this, - "No species tree loaded", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; + void writeToFile( final Phylogeny t ) { + if ( t == null ) { + return; } - else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) { - JOptionPane.showMessageDialog( this, - "Species tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; + String initial_filename = null; + if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { + try { + initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath(); + } + catch ( final IOException e ) { + initial_filename = null; + } } - else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not completely binary", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return false; + if ( !ForesterUtil.isEmpty( initial_filename ) ) { + _save_filechooser.setSelectedFile( new File( initial_filename ) ); } else { - return true; + _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() == MainFrame.nhfilter ) { + exception = writeAsNewHampshire( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + exception = writeAsPhyloXml( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.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 ); + } } } - boolean isSubtreeDisplayed() { - if ( getCurrentTreePanel() != null ) { - if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { - JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); - return true; + 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 ); } - return false; } - void midpointRoot() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().midpointRoot(); + void writeToPdf( final Phylogeny t ) { + if ( ( t == null ) || t.isEmpty() ) { + return; } - } - - void printPhylogenyToPdf( final String file_name ) { - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel() - .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() ); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().repaint(); + String initial_filename = ""; + if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); } - 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() ); - } + if ( initial_filename.indexOf( '.' ) > 0 ) { + initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); } - catch ( final IOException e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + 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 ); } - if ( !error ) { - if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { - JOptionPane.showMessageDialog( this, - "Wrote PDF to: " + pdf_written_to, - "Information", - JOptionPane.INFORMATION_MESSAGE ); + 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" ); } - else { - JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to PDF file: \"" - + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); + 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() ); } - if ( !getOptions().isPrintUsingActualSize() ) { - getControlPanel().showWhole(); - } - } - - void readPhylogeniesFromWebservice( final int i ) { - final UrlTreeReader reader = new UrlTreeReader( this, i ); - new Thread( reader ).start(); } - void removeAllTextFrames() { - for( final TextFrame tf : _textframes ) { - if ( tf != null ) { - tf.close(); + private void annotateSequences() { + if ( getCurrentTreePanel() != null ) { + List nodes = null; + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) + || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + } + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( this, + "Need to select nodes, either via direct selection or via the \"Search\" function", + "No nodes selected for annotation", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final JTextField ref_field = new JTextField( 10 ); + final JTextField desc_filed = new JTextField( 20 ); + ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" + : getPreviousNodeAnnotationReference() ); + final JPanel my_panel = new JPanel(); + my_panel.add( new JLabel( "Reference " ) ); + my_panel.add( ref_field ); + my_panel.add( Box.createHorizontalStrut( 15 ) ); + my_panel.add( new JLabel( "Description " ) ); + my_panel.add( desc_filed ); + final int result = JOptionPane.showConfirmDialog( null, + my_panel, + "Enter the sequence annotation(s) for the " + + nodes.size() + " selected nodes", + JOptionPane.OK_CANCEL_OPTION ); + if ( result == JOptionPane.OK_OPTION ) { + String ref = ref_field.getText(); + String desc = desc_filed.getText(); + if ( !ForesterUtil.isEmpty( ref ) ) { + ref = ref.trim(); + ref = ref.replaceAll( "\\s+", " " ); + if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) ) + || ( ref.length() < 3 ) ) { + JOptionPane.showMessageDialog( this, + "Reference needs to be in the form of \"GO:1234567\"", + "Illegal Format for Annotation Reference", + JOptionPane.ERROR_MESSAGE ); + return; + } + } + if ( ref != null ) { + setPreviousNodeAnnotationReference( ref ); + } + if ( desc != null ) { + desc = desc.trim(); + desc = desc.replaceAll( "\\s+", " " ); + } + if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { + for( final PhylogenyNode n : nodes ) { + ForesterUtil.ensurePresenceOfSequence( n ); + final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() + : new Annotation( ref ); + if ( !ForesterUtil.isEmpty( desc ) ) { + ann.setDesc( desc ); + } + n.getNodeData().getSequence().addAnnotation( ann ); + } + } + getMainPanel().getControlPanel().showAnnotations(); + } } } - _textframes.clear(); - } - - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void removeVisualStyles() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); - } - } - - void resetSearch() { - getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); - getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); - } - - void setConfiguration( final Configuration configuration ) { - _configuration = configuration; - } - - void setCurrentDir( final File current_dir ) { - _current_dir = current_dir; - } - - void setInferenceManager( final InferenceManager i ) { - _inference_manager = i; - } - - void setOptions( final Options options ) { - _options = options; - } - - private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { - _previous_node_annotation_ref = previous_node_annotation_ref; - } - - void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { - setTypeMenuToAllUnselected(); - switch ( type ) { - case CIRCULAR: - _circular_type_cbmi.setSelected( true ); - break; - case CONVEX: - _convex_type_cbmi.setSelected( true ); - break; - case CURVED: - _curved_type_cbmi.setSelected( true ); - break; - case EURO_STYLE: - _euro_type_cbmi.setSelected( true ); - break; - case ROUNDED: - _rounded_type_cbmi.setSelected( true ); - break; - case RECTANGULAR: - _rectangular_type_cbmi.setSelected( true ); - break; - case TRIANGULAR: - _triangular_type_cbmi.setSelected( true ); - break; - case UNROOTED: - _unrooted_type_cbmi.setSelected( true ); - break; - default: - throw new IllegalArgumentException( "unknown type: " + type ); - } - } - - final void setSpeciesTree( final Phylogeny species_tree ) { - _species_tree = species_tree; - } - - void setTypeMenuToAllUnselected() { - _convex_type_cbmi.setSelected( false ); - _curved_type_cbmi.setSelected( false ); - _euro_type_cbmi.setSelected( false ); - _rounded_type_cbmi.setSelected( false ); - _triangular_type_cbmi.setSelected( false ); - _rectangular_type_cbmi.setSelected( false ); - _unrooted_type_cbmi.setSelected( false ); - _circular_type_cbmi.setSelected( false ); - } - - public void showTextFrame( final String s, final String title ) { - checkTextFrames(); - _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); - } - - public void showWhole() { - _mainpanel.getControlPanel().showWhole(); - } - - void switchColors() { - final TreeColorSet colorset = _mainpanel.getTreeColorSet(); - final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); - csc.setVisible( true ); } - void taxColor() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().taxColor(); - } + private void chooseFont() { + final FontChooser fc = new FontChooser(); + fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); + fc.showDialog( this, "Select the Base Font" ); + getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); } - void typeChanged( final Object o ) { - updateTypeCheckboxes( getOptions(), o ); - updateOptions( getOptions() ); - if ( getCurrentTreePanel() != null ) { - final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType(); - final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType(); - if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) - || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) - || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) - || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) { - getCurrentTreePanel().getControlPanel().showWhole(); - } - if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true ); + private void chooseMinimalConfidence() { + final String s = ( String ) JOptionPane + .showInputDialog( this, + "Please enter the minimum for confidence values to be displayed.\n" + + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getMinConfidenceValue() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } } else { - getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false ); + success = false; } - getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() ); - updateScreenTextAntialias( getMainPanel().getTreePanels() ); - if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) { - if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false ); - } - else { - getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true ); - } + if ( success && ( m >= 0.0 ) ) { + getOptions().setMinConfidenceValue( m ); } } } - void updateOptions( final Options options ) { - options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); - options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) - && _background_gradient_cbmi.isSelected() ); - options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); - options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) - && _show_annotation_ref_source.isSelected() ); - options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) - && _abbreviate_scientific_names.isSelected() ); - options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) - && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) - && _show_default_node_shapes_internal_cbmi.isSelected() ); - options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) - && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) - && _show_default_node_shapes_for_marked_cbmi.isSelected() ); - if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); + private void deleteSelectedNodes( final boolean delete ) { + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { + return; } - else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); + final List nodes = new ArrayList(); + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + for( final PhylogenyNode n : all_selected_nodes ) { + if ( n.isExternal() ) { + nodes.add( n ); + } + } } - else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); + String function = "Retain"; + if ( delete ) { + function = "Delete"; } - options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) - && _search_case_senstive_cbmi.isSelected() ); - if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { - options.setShowScale( _show_scale_cbmi.isSelected() ); + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( this, + "Need to select external nodes, either via direct selection or via the \"Search\" function", + "No external nodes selected to " + function.toLowerCase(), + JOptionPane.ERROR_MESSAGE ); + return; } - if ( _label_direction_cbmi != null ) { - if ( _label_direction_cbmi.isSelected() ) { - options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); + final int todo = nodes.size(); + final int ext = phy.getNumberOfExternalNodes(); + int res = todo; + if ( delete ) { + res = ext - todo; + } + if ( res < 1 ) { + JOptionPane.showMessageDialog( this, + "Cannot delete all nodes", + "Attempt to delete all nodes ", + JOptionPane.ERROR_MESSAGE ); + return; + } + final int result = JOptionPane.showConfirmDialog( null, function + " " + todo + + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res + + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); + if ( result == JOptionPane.OK_OPTION ) { + if ( !delete ) { + final List to_delete = new ArrayList(); + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( !nodes.contains( n ) ) { + to_delete.add( n ); + } + } + for( final PhylogenyNode n : to_delete ) { + phy.deleteSubtree( n, true ); + } } else { - options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); + for( final PhylogenyNode n : nodes ) { + phy.deleteSubtree( n, true ); + } } + resetSearch(); + getCurrentTreePanel().setNodeInPreorderToNull(); + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().setEdited( true ); + repaint(); } - options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); - options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) - && _show_confidence_stddev_cbmi.isSelected() ); - if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { - options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); - } - options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) - && ( _print_using_actual_size_cbmi.isSelected() ) ); - options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) - && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); - options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); - if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) - && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { - options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); - } - else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) - && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { - options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + } + + private void doUpdateProcessMenu() { + if ( _process_pool.size() > 0 ) { + if ( _process_menu == null ) { + _process_menu = createMenu( "", getConfiguration() ); + _process_menu.setForeground( Color.RED ); + } + _process_menu.removeAll(); + final String text = "processes running: " + _process_pool.size(); + _process_menu.setText( text ); + _jmenubar.add( _process_menu ); + for( int i = 0; i < _process_pool.size(); ++i ) { + final ProcessRunning p = _process_pool.getProcessByIndex( i ); + _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + } } else { - options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); + if ( _process_menu != null ) { + _process_menu.removeAll(); + _jmenubar.remove( _process_menu ); + } } - options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) - && _print_black_and_white_cbmi.isSelected() ); - options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) - && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); - if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { - options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + _jmenubar.validate(); + _jmenubar.repaint(); + repaint(); + } + + private String getPreviousNodeAnnotationReference() { + return _previous_node_annotation_ref; + } + + static void print( final TreePanel tp, + final Options op, + + final Component c + ) { + if ( ( tp == null ) || ( tp.getPhylogeny() == null ) + || tp.getPhylogeny().isEmpty() ) { + return; } - else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { - options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + if ( !op.isPrintUsingActualSize() ) { + tp.calcParametersForPainting( op.getPrintSizeX() - 80, + op.getPrintSizeY() - 140 ); + tp.resetPreferredSize(); + tp.repaint(); } - else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { - options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); + final String job_name = Constants.PRG_NAME; + boolean error = false; + String printer_name = null; + try { + printer_name = Printer.print( tp, job_name ); } - else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { - options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + catch ( final Exception e ) { + error = true; + JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); } - options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) - && _replace_underscores_cbmi.isSelected() ); - options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) - && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); - options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) - && _search_whole_words_only_cbmi.isSelected() ); - options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); - options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) - && _inverse_search_result_cbmi.isSelected() ); - if ( _graphics_export_visible_only_cbmi != null ) { - options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); - if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) { - _graphics_export_using_actual_size_cbmi.setSelected( true ); - _graphics_export_using_actual_size_cbmi.setEnabled( false ); - } - else { - _graphics_export_using_actual_size_cbmi.setEnabled( true ); + if ( !error && ( printer_name != null ) ) { + String msg = "Printing data sent to printer"; + if ( printer_name.length() > 1 ) { + msg += " [" + printer_name + "]"; } + JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); } - if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - } - else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + if ( !op.isPrintUsingActualSize() ) { + tp.getControlPanel().showWhole(); } - else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); } - else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + } + + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); } - else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + } + + private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { + _previous_node_annotation_ref = previous_node_annotation_ref; + } + + private void writeAllToFile() { + if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { + return; } - else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _save_filechooser.setCurrentDirectory( my_dir ); } - else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { - options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + _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 ); + } } - if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { - options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + + /** + * Display the about box. + */ + static void about() { + final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); + about.append( "Copyright (C) 2014 Christian M Zmasek\n" ); + about.append( "All Rights Reserved\n" ); + about.append( "License: GNU Lesser General Public License (LGPL)\n" ); + about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); + about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); + about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); + about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); + if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { + about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" ); } - if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { - options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH ) + && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) { + about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + + ForesterUtil.OS_VERSION + "]\n" ); } + final Runtime rt = java.lang.Runtime.getRuntime(); + final long free_memory = rt.freeMemory() / 1000000; + final long total_memory = rt.totalMemory() / 1000000; + about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" ); + about.append( "[locale: " + Locale.getDefault() + "]\n" ); + about.append( "References:\n" ); + about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" ); + about.append( "For more information & download:\n" ); + about.append( Constants.APTX_WEB_SITE + "\n" ); + about.append( "Documentation:\n" ); + about.append( Constants.APTX_DOC_SITE + "\n" ); + about.append( "Comments: " + Constants.AUTHOR_EMAIL ); + JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); } - public void updateProcessMenu() { - // In general Swing is not thread safe. - // See "Swing's Threading Policy". - SwingUtilities.invokeLater( new Runnable() { - - @Override - public void run() { - doUpdateProcessMenu(); + static void chooseNodeSize( final Options options, final Component parent ) { + final String s = ( String ) JOptionPane.showInputDialog( parent, + "Please enter the default size for node shapes.\n" + + "[current value: " + + options.getDefaultNodeShapeSize() + "]\n", + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } } - } ); + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + final short size = ForesterUtil.roundToShort( m ); + if ( size >= 0.0 ) { + options.setDefaultNodeShapeSize( size ); + } + } + } } - void updateTypeCheckboxes( final Options options, final Object o ) { - setTypeMenuToAllUnselected(); - ( ( JCheckBoxMenuItem ) o ).setSelected( true ); + static String createCurrentFontDesc( final TreeFontSet tree_font_set ) { + return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize(); } - void viewAsNexus() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "Nexus"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), - title ); + static JMenu createMenu( final String title, final Configuration conf ) { + final JMenu jmenu = new JMenu( title ); + if ( !conf.isUseNativeUI() ) { + jmenu.setFont( MainFrame.menu_font ); + jmenu.setBackground( conf.getGuiMenuBackgroundColor() ); + jmenu.setForeground( conf.getGuiMenuTextColor() ); } + return jmenu; } - void viewAsNH() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "New Hampshire"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) { + label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) ); + if ( !configuration.isUseNativeUI() ) { + label.setBackground( configuration.getGuiMenuBackgroundColor() ); + label.setForeground( configuration.getGuiMenuTextColor() ); + label.setOpaque( true ); } + label.setSelected( false ); + label.setEnabled( false ); + return label; } - void viewAsXML() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "phyloXML"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; - } - showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); + static void cycleNodeFill( final Options op ) { + switch ( op.getDefaultNodeFill() ) { + case GRADIENT: + op.setDefaultNodeFill( NodeFill.SOLID ); + break; + case NONE: + op.setDefaultNodeFill( NodeFill.GRADIENT ); + break; + case SOLID: + op.setDefaultNodeFill( NodeFill.NONE ); + break; + default: + throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); } } - 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 ); + static void cycleNodeShape( final Options op ) { + switch ( op.getDefaultNodeShape() ) { + case CIRCLE: + op.setDefaultNodeShape( NodeShape.RECTANGLE ); + break; + case RECTANGLE: + op.setDefaultNodeShape( NodeShape.CIRCLE ); + break; + default: + throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); } - return exception; } - boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() ); + static void cycleOverview( final Options op, final TreePanel tree_panel ) { + switch ( op.getOvPlacement() ) { + case LOWER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); + break; + case LOWER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); + break; + case UPPER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); + break; + case UPPER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); + break; + default: + throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); + if ( tree_panel != null ) { + tree_panel.updateOvSettings(); } - return exception; } - boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( file, t, 0 ); + static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { + mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" ); } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); + else { + mi.setText( "Cycle Node Return Data..." ); } - return exception; } - void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight() ); - 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 ); + static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); } - 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 ); - } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); } - _contentpane.repaint(); } - void writeToFile( final Phylogeny t ) { - if ( t == null ) { - return; + static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); } - String initial_filename = null; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - try { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath(); - } - catch ( final IOException e ) { - initial_filename = null; - } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); } - if ( !ForesterUtil.isEmpty( initial_filename ) ) { - _save_filechooser.setSelectedFile( new File( initial_filename ) ); + } + + static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { + mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); } else { - _save_filechooser.setSelectedFile( new File( "" ) ); + mi.setText( "Cycle Overview Placement..." ); } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _save_filechooser.setCurrentDirectory( my_dir ); + } + + static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { + if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { + mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + + ")" ); } - 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() == MainFrame.nhfilter ) { - exception = writeAsNewHampshire( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { - exception = writeAsPhyloXml( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrame.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 ); - } + else { + mi.setText( "Select Color Scheme..." ); } } - void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) { - if ( ( t == null ) || t.isEmpty() ) { - return; + static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) { + mi.setText( "Select Default Font... (current: " + font_desc + ")" ); + } + + 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 setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) { + if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { + mi.setEnabled( true ); } - String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); + else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { + mi.setEnabled( true ); } - if ( initial_filename.indexOf( '.' ) > 0 ) { - initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); + else { + mi.setEnabled( false ); } - 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 ); + mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); + } + + static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { + mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); + } + + static void updateScreenTextAntialias( final List treepanels ) { + for( final TreePanel tree_panel : treepanels ) { + tree_panel.setTextAntialias(); } - 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; + } + + private static void cycleNodeDataReturn( final Options op, final Configuration conf ) { + switch ( op.getExtDescNodeDataToReturn() ) { + case UNKNOWN: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); + break; + case DOMAINS_ALL: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); + break; + case DOMAINS_COLLAPSED_PER_PROTEIN: + op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); + break; + case SEQ_ANNOTATIONS: + op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); + break; + case GO_TERM_IDS: + op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); + break; + case SEQUENCE_MOL_SEQ_FASTA: + if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) { + op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); } else { - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } - } - writePhylogenyToGraphicsFile( file.toString(), type ); + break; + default: + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } } +} - 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() ); - } +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)"; } } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 29a0a57..2588e95 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -435,27 +435,11 @@ public final class MainFrameApplication extends MainFrame { else if ( o == _new_item ) { newTree(); } - else if ( o == _save_all_item ) { - writeAllToFile(); - } + else if ( o == _close_item ) { closeCurrentPane(); } - else if ( o == _write_to_jpg_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); - } - 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(); } @@ -1731,38 +1715,7 @@ public final class MainFrameApplication extends MainFrame { } } - private void print() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) - || getCurrentTreePanel().getPhylogeny().isEmpty() ) { - return; - } - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80, - getOptions().getPrintSizeY() - 140 ); - 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(); - } - } + public void readMsaFromFile() { // Set an initial directory if none set yet @@ -2300,61 +2253,5 @@ public final class MainFrameApplication extends MainFrame { 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 ); - } - } - } + } // MainFrameApplication. -- 1.7.10.2