X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=6743505f586690b010f84127b648dea1903221af;hb=b0fd64a5d558885627ba7a7295d9ef612fe76cd0;hp=2796e00a54aa7c977b8244e148237b415e9f25c7;hpb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 2796e00..6743505 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -18,6 +18,7 @@ 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;
@@ -43,6 +44,7 @@ import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDIException;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
+import org.forester.util.WindowsUtils;
 
 // Use like this:
 // <applet archive="forester.jar"
@@ -61,7 +63,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private final static String         NAME             = "ArchaeopteryxE";
     private static final long           serialVersionUID = -1220055577935759443L;
     private Configuration               _configuration;
-    private MainPanelApplets            _mainpanel;
+    private MainPanel                   _mainpanel;
     private JMenuBar                    _jmenubar;
     private JMenu                       _options_jmenu;
     private JMenu                       _font_size_menu;
@@ -115,6 +117,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
+    private JCheckBoxMenuItem           _search_with_regex_cbmi;
     private JCheckBoxMenuItem           _show_overview_cbmi;
     private JMenuItem                   _choose_minimal_confidence_mi;
     private JMenuItem                   _collapse_species_specific_subtrees;
@@ -134,6 +137,27 @@ 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:
+    private JMenuItem                   _save_item;
+    private JMenuItem                   _print_item;
+    private JMenuItem                   _write_to_pdf_item;
+    private JMenuItem                   _write_to_jpg_item;
+    private JMenuItem                   _write_to_gif_item;
+    private JMenuItem                   _write_to_tif_item;
+    private JMenuItem                   _write_to_png_item;
+    private JMenuItem                   _write_to_bmp_item;
+    private JMenu                       _file_jmenu;
+    private JFileChooser                _writetopdf_filechooser;
+    private File                        _current_dir;
+    private JFileChooser                _save_filechooser;
+    private JFileChooser                _writetographics_filechooser;
+    private JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
+    private JCheckBoxMenuItem           _antialias_print_cbmi;
+    private JCheckBoxMenuItem           _print_black_and_white_cbmi;
+    private JCheckBoxMenuItem           _print_using_actual_size_cbmi;
+    private JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
+    private JMenuItem                   _print_size_mi;
+    private JMenuItem                   _choose_pdf_width_mi;
 
     @Override
     public void actionPerformed( final ActionEvent e ) {
@@ -228,10 +252,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
         }
         else if ( o == _cycle_node_fill_mi ) {
-            MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+            MainFrame.cycleNodeFill( getOptions() );
         }
         else if ( o == _cycle_node_shape_mi ) {
-            MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+            MainFrame.cycleNodeShape( getOptions() );
         }
         else if ( o == _non_lined_up_cladograms_rbmi ) {
             updateOptions( getOptions() );
@@ -251,6 +275,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             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();
@@ -260,6 +287,17 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             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() );
         }
@@ -307,42 +345,42 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
         else if ( o == _help_item ) {
             try {
-                AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
+                AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, true, this );
             }
             catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
         else if ( o == _website_item ) {
             try {
-                AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
+                AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this );
             }
             catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
         else if ( o == _phyloxml_website_item ) {
             try {
-                AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
+                AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this );
             }
             catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
         else if ( o == _aptx_ref_item ) {
             try {
-                AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
+                AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this );
             }
             catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
         else if ( o == _phyloxml_ref_item ) {
             try {
-                AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
+                AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this );
             }
             catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
         else if ( o == _color_by_taxonomic_group_cbmi ) {
@@ -360,6 +398,112 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
             updateOptions( getOptions() );
         }
+        else if ( o == _write_to_pdf_item ) {
+            final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(),
+                                                        getMainPanel(),
+                                                        _writetopdf_filechooser,
+                                                        _current_dir,
+                                                        getContentPane(),
+                                                        this );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _write_to_jpg_item ) {
+            final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+                                                                 GraphicsExportType.JPG,
+                                                                 _mainpanel,
+                                                                 _writetographics_filechooser,
+                                                                 this,
+                                                                 getContentPane(),
+                                                                 _current_dir );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _write_to_gif_item ) {
+            final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+                                                                 GraphicsExportType.GIF,
+                                                                 _mainpanel,
+                                                                 _writetographics_filechooser,
+                                                                 this,
+                                                                 getContentPane(),
+                                                                 _current_dir );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _write_to_tif_item ) {
+            final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+                                                                 GraphicsExportType.TIFF,
+                                                                 _mainpanel,
+                                                                 _writetographics_filechooser,
+                                                                 this,
+                                                                 getContentPane(),
+                                                                 _current_dir );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _write_to_bmp_item ) {
+            final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+                                                                 GraphicsExportType.BMP,
+                                                                 _mainpanel,
+                                                                 _writetographics_filechooser,
+                                                                 this,
+                                                                 getContentPane(),
+                                                                 _current_dir );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _write_to_png_item ) {
+            final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+                                                                 GraphicsExportType.PNG,
+                                                                 _mainpanel,
+                                                                 _writetographics_filechooser,
+                                                                 this,
+                                                                 getContentPane(),
+                                                                 _current_dir );
+            if ( curr_dir != null ) {
+                setCurrentDir( curr_dir );
+            }
+        }
+        else if ( o == _print_item ) {
+            MainFrame.print( getCurrentTreePanel(), getOptions(), this );
+        }
+        else if ( o == _save_item ) {
+            final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(),
+                                                        getMainPanel(),
+                                                        _save_filechooser,
+                                                        _current_dir,
+                                                        getContentPane(),
+                                                        this );
+            if ( new_dir != null ) {
+                setCurrentDir( new_dir );
+            }
+        }
+        else if ( o == _graphics_export_visible_only_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        else if ( o == _antialias_print_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        else if ( o == _print_black_and_white_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        else if ( o == _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();
     }
 
@@ -377,7 +521,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
      * 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() {
@@ -394,7 +538,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     /**
      * This method returns the current phylogeny as a string in the chosen format
-     * 
+     *
      * @param format must be NH, NHX, NEXUS or PHYLOXML
      * @return the phylogeny string
      * @author Herve Menager
@@ -421,10 +565,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     }
 
     /**
-     * This method returns a view of the current phylogeny in a chosen 
+     * This method returns a view of the current phylogeny in a chosen
      * graphics format, base64-encoded in a string so that in can be used
      * from javascript.
-     * 
+     *
      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
      * @return the phylogeny string
      * @author Herve Menager
@@ -460,18 +604,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     @Override
     public void init() {
-        final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+        _writetopdf_filechooser = new JFileChooser();
+        _writetopdf_filechooser.setMultiSelectionEnabled( false );
+        _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );
+        _writetographics_filechooser = new JFileChooser();
+        _writetographics_filechooser.setMultiSelectionEnabled( false );
+        _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
+        _save_filechooser = new JFileChooser();
+        _save_filechooser.setMultiSelectionEnabled( false );
+        _save_filechooser.setFileFilter( MainFrame.xmlfilter );
+        _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
+        _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
+        _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
+        try {
+            final String home_dir = System.getProperty( "user.home" );
+            _save_filechooser.setCurrentDirectory( new File( home_dir ) );
+            _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
+            _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            // Do nothing. Not important.
+        }
+        final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
         final Configuration configuration = new Configuration( config_filename, true, true, true );
         setConfiguration( configuration );
         setOptions( Options.createInstance( configuration ) );
         setupUI();
-        final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+        final String tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
-                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+                    + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
-                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+                    + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
             return;
         }
         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
@@ -488,7 +654,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
         if ( phys_url == null ) {
             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
-                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+                    + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
             JOptionPane.showMessageDialog( this,
                                            NAME + ": Could not create URL from: \"" + tree_url_str,
                                            "Failed to create URL",
@@ -533,7 +699,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
         }
         //
-        final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
+        final String species_tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
             Phylogeny[] species_trees = null;
@@ -566,12 +732,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 }
             }
         }
-        //
         try {
             setVisible( false );
             setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
             _jmenubar = new JMenuBar();
             if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+                buildFileMenu();
                 if ( !getConfiguration().isUseNativeUI() ) {
                     _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
                 }
@@ -594,10 +760,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 @Override
                 public void componentResized( final ComponentEvent e ) {
                     if ( getMainPanel().getCurrentTreePanel() != null ) {
-                        getMainPanel().getCurrentTreePanel()
-                                .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
-                                                            getMainPanel().getCurrentTreePanel().getHeight(),
-                                                            getOptions().isAllowFontSizeChange() );
+                        getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
+                                                                                                .getCurrentTreePanel()
+                                                                                                .getWidth(),
+                                                                                        getMainPanel()
+                                                                                                .getCurrentTreePanel()
+                                                                                                .getHeight() );
                     }
                 }
             } );
@@ -633,11 +801,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                     .getRelevantSequenceRelationTypes() ) {
                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
             }
-            final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+            final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
             if ( default_relation != null ) {
                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
             }
-            final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+            final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
             if ( default_sequence != null ) {
                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
             }
@@ -668,19 +836,227 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         AptxUtil.printAppletMessage( NAME, "started" );
     }
 
+    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() );
+    }
+
+    private void chooseMinimalConfidence() {
+        final String s = ( String ) JOptionPane
+                .showInputDialog( this,
+                                  "Please the minimum for confidence values to be displayed.\n" + "[current value: "
+                                          + getOptions().getMinConfidenceValue() + "]\n",
+                                  "Minimal Confidence Value",
+                                  JOptionPane.QUESTION_MESSAGE,
+                                  null,
+                                  null,
+                                  getOptions().getMinConfidenceValue() );
+        if ( !ForesterUtil.isEmpty( s ) ) {
+            boolean success = true;
+            double m = 0.0;
+            final String m_str = s.trim();
+            if ( !ForesterUtil.isEmpty( m_str ) ) {
+                try {
+                    m = Double.parseDouble( m_str );
+                }
+                catch ( final Exception ex ) {
+                    success = false;
+                }
+            }
+            else {
+                success = false;
+            }
+            if ( success && ( m >= 0.0 ) ) {
+                getOptions().setMinConfidenceValue( m );
+            }
+        }
+    }
+
+    private void choosePdfWidth() {
+        final String s = ( String ) JOptionPane.showInputDialog( this,
+                                                                 "Please enter the default line width for PDF export.\n"
+                                                                         + "[current value: "
+                                                                         + getOptions().getPrintLineWidth() + "]\n",
+                                                                         "Line Width for PDF Export",
+                                                                         JOptionPane.QUESTION_MESSAGE,
+                                                                         null,
+                                                                         null,
+                                                                         getOptions().getPrintLineWidth() );
+        if ( !ForesterUtil.isEmpty( s ) ) {
+            boolean success = true;
+            float f = 0.0f;
+            final String m_str = s.trim();
+            if ( !ForesterUtil.isEmpty( m_str ) ) {
+                try {
+                    f = Float.parseFloat( m_str );
+                }
+                catch ( final Exception ex ) {
+                    success = false;
+                }
+            }
+            else {
+                success = false;
+            }
+            if ( success && ( f > 0.0 ) ) {
+                getOptions().setPrintLineWidth( f );
+            }
+        }
+    }
+
+    private void choosePrintSize() {
+        final String s = ( String ) JOptionPane.showInputDialog( this,
+                                                                 "Please enter values for width and height,\nseparated by a comma.\n"
+                                                                         + "[current values: "
+                                                                         + getOptions().getPrintSizeX() + ", "
+                                                                         + getOptions().getPrintSizeY() + "]\n"
+                                                                         + "[A4: " + AptxConstants.A4_SIZE_X + ", "
+                                                                         + AptxConstants.A4_SIZE_Y + "]\n" + "[US Letter: "
+                                                                         + AptxConstants.US_LETTER_SIZE_X + ", "
+                                                                         + AptxConstants.US_LETTER_SIZE_Y + "]",
+                                                                         "Default Size for Graphics Export",
+                                                                         JOptionPane.QUESTION_MESSAGE,
+                                                                         null,
+                                                                         null,
+                                                                         getOptions().getPrintSizeX() + ", "
+                                                                                 + getOptions().getPrintSizeY() );
+        if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
+            boolean success = true;
+            int x = 0;
+            int y = 0;
+            final String[] str_ary = s.split( "," );
+            if ( str_ary.length == 2 ) {
+                final String x_str = str_ary[ 0 ].trim();
+                final String y_str = str_ary[ 1 ].trim();
+                if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
+                    try {
+                        x = Integer.parseInt( x_str );
+                        y = Integer.parseInt( y_str );
+                    }
+                    catch ( final Exception ex ) {
+                        success = false;
+                    }
+                }
+                else {
+                    success = false;
+                }
+            }
+            else {
+                success = false;
+            }
+            if ( success && ( x > 1 ) && ( y > 1 ) ) {
+                getOptions().setPrintSizeX( x );
+                getOptions().setPrintSizeY( y );
+            }
+        }
+    }
+
+    private void 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 );
+        }
+    }
+
+    private Phylogeny getSpeciesTree() {
+        return _species_tree;
+    }
+
+    private boolean isScreenAntialias() {
+        return true;
+    }
+
+    private void removeBranchColors() {
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {
+            AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+        }
+    }
+
+    private void removeVisualStyles() {
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {
+            AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+        }
+    }
+
+    private void setMainPanel( final MainPanelApplets main_panel ) {
+        _mainpanel = main_panel;
+    }
+
+    private void setSpeciesTree( final Phylogeny species_tree ) {
+        _species_tree = species_tree;
+    }
+
+    private void setupUI() {
+        try {
+            if ( getConfiguration().isUseNativeUI() ) {
+                UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+            }
+            else {
+                UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+            }
+        }
+        catch ( final UnsupportedLookAndFeelException e ) {
+            AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+        }
+        catch ( final ClassNotFoundException e ) {
+            AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+        }
+        catch ( final InstantiationException e ) {
+            AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
+        }
+        catch ( final IllegalAccessException e ) {
+            AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+        }
+        catch ( final Exception e ) {
+            AptxUtil.dieWithSystemError( e.toString() );
+        }
+    }
+
     void buildAnalysisMenu() {
         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
         customizeJMenuItem( _gsdi_item );
         customizeJMenuItem( _gsdir_item );
-        //  _analysis_menu.addSeparator();
-        //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
-        //  customizeJMenuItem( _lineage_inference );
-        //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+        _analysis_menu.addSeparator();
         _jmenubar.add( _analysis_menu );
     }
 
+    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..." ) );
+        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 );
+        _jmenubar.add( _file_jmenu );
+    }
+
     void buildFontSizeMenu() {
         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
@@ -729,6 +1105,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
+                setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+                setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
@@ -759,7 +1137,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
         _options_jmenu
-                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
@@ -790,8 +1168,34 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu
                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
+        _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+        _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
         _options_jmenu
                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
+        //
+        _options_jmenu.addSeparator();
+        _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
+                                                                getConfiguration() ) );
+        _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
+        _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
+        _options_jmenu
+                .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
+        _options_jmenu
+                .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
+        _options_jmenu
+                .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+        _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
+        _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
+        //
+        customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
+        customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
+        customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
+        customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
+        customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
+                .isGraphicsExportUsingActualSize() );
+        customizeJMenuItem( _print_size_mi );
+        customizeJMenuItem( _choose_pdf_width_mi );
+        //
         customizeJMenuItem( _choose_font_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _switch_colors_mi );
@@ -823,6 +1227,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+        customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
@@ -926,12 +1331,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     }
 
     void customizeJMenuItem( final JMenuItem jmi ) {
-        jmi.setFont( MainFrame.menu_font );
-        if ( !getConfiguration().isUseNativeUI() ) {
-            jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
-            jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+        if ( jmi != null ) {
+            jmi.setFont( MainFrame.menu_font );
+            if ( !getConfiguration().isUseNativeUI() ) {
+                jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+                jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+            }
+            jmi.addActionListener( this );
         }
-        jmi.addActionListener( this );
     }
 
     void displayBasicInformation() {
@@ -1091,6 +1498,28 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         return _configuration;
     }
 
+    File getCurrentDir() {
+        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+            if ( ForesterUtil.isWindows() ) {
+                try {
+                    _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
+                }
+                catch ( final Exception e ) {
+                    _current_dir = null;
+                }
+            }
+        }
+        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+            if ( System.getProperty( "user.home" ) != null ) {
+                _current_dir = new File( System.getProperty( "user.home" ) );
+            }
+            else if ( System.getProperty( "user.dir" ) != null ) {
+                _current_dir = new File( System.getProperty( "user.dir" ) );
+            }
+        }
+        return _current_dir;
+    }
+
     TreePanel getCurrentTreePanel() {
         return getMainPanel().getCurrentTreePanel();
     }
@@ -1099,6 +1528,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         return _label_direction_cbmi;
     }
 
+    MainPanel getMainPanel() {
+        return _mainpanel;
+    }
+
     Options getOtions() {
         return _options;
     }
@@ -1195,6 +1628,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _configuration = configuration;
     }
 
+    void setCurrentDir( final File current_dir ) {
+        _current_dir = current_dir;
+    }
+
     void setOptions( final Options options ) {
         _options = options;
     }
@@ -1341,8 +1778,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 && _show_confidence_stddev_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() );
+        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() );
+        options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
+                                       && _print_black_and_white_cbmi.isSelected() );
         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
         }
@@ -1376,6 +1821,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
             options.setLineUpRendarableNodeData( _line_up_renderable_data_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 );
+            }
+        }
     }
 
     void updateTypeCheckboxes( final Options options, final Object o ) {
@@ -1417,112 +1872,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
     }
 
-    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() );
-    }
-
-    private void chooseMinimalConfidence() {
-        final String s = ( String ) JOptionPane
-                .showInputDialog( this,
-                                  "Please the minimum for confidence values to be displayed.\n" + "[current value: "
-                                          + getOptions().getMinConfidenceValue() + "]\n",
-                                  "Minimal Confidence Value",
-                                  JOptionPane.QUESTION_MESSAGE,
-                                  null,
-                                  null,
-                                  getOptions().getMinConfidenceValue() );
-        if ( !ForesterUtil.isEmpty( s ) ) {
-            boolean success = true;
-            double m = 0.0;
-            final String m_str = s.trim();
-            if ( !ForesterUtil.isEmpty( m_str ) ) {
-                try {
-                    m = Double.parseDouble( m_str );
-                }
-                catch ( final Exception ex ) {
-                    success = false;
-                }
-            }
-            else {
-                success = false;
-            }
-            if ( success && ( m >= 0.0 ) ) {
-                getOptions().setMinConfidenceValue( m );
-            }
-        }
-    }
-
-    private void 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 );
-        }
-    }
-
-    MainPanel getMainPanel() {
-        return _mainpanel;
-    }
-
-    private Phylogeny getSpeciesTree() {
-        return _species_tree;
-    }
-
-    private boolean isScreenAntialias() {
-        return true;
-    }
-
-    private void removeBranchColors() {
-        if ( getMainPanel().getCurrentPhylogeny() != null ) {
-            AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
-        }
-    }
-
-    private void removeVisualStyles() {
-        if ( getMainPanel().getCurrentPhylogeny() != null ) {
-            AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
-        }
-    }
-
-    private void setMainPanel( final MainPanelApplets main_panel ) {
-        _mainpanel = main_panel;
-    }
-
-    private void setSpeciesTree( final Phylogeny species_tree ) {
-        _species_tree = species_tree;
+    static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
+        mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
+                + o.getPrintSizeY() + ")" );
     }
 
-    private void setupUI() {
-        try {
-            if ( getConfiguration().isUseNativeUI() ) {
-                UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
-            }
-            else {
-                UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
-            }
-        }
-        catch ( final UnsupportedLookAndFeelException e ) {
-            AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
-        }
-        catch ( final ClassNotFoundException e ) {
-            AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
-        }
-        catch ( final InstantiationException e ) {
-            AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
-        }
-        catch ( final IllegalAccessException e ) {
-            AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
-        }
-        catch ( final Exception e ) {
-            AptxUtil.dieWithSystemError( e.toString() );
-        }
+    static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
+        mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
     }
 
     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {