X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=6743505f586690b010f84127b648dea1903221af;hb=b0fd64a5d558885627ba7a7295d9ef612fe76cd0;hp=daa014785bbc6e1289afedd118b3e18dd5147f6c;hpb=5b0302dbbd662402f68e5dee1c1e8d457144f53f;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index daa0147..6743505 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -138,13 +138,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JCheckBoxMenuItem _right_line_up_domains_cbmi; private JCheckBoxMenuItem _line_up_renderable_data_cbmi; // file menu: - private JMenuItem _open_item; - private JMenuItem _open_url_item; private JMenuItem _save_item; - private JMenuItem _save_all_item; - private JMenuItem _close_item; - private JMenuItem _exit_item; - private JMenuItem _new_item; private JMenuItem _print_item; private JMenuItem _write_to_pdf_item; private JMenuItem _write_to_jpg_item; @@ -157,64 +151,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private File _current_dir; private JFileChooser _save_filechooser; private JFileChooser _writetographics_filechooser; - - void setCurrentDir( final File current_dir ) { - _current_dir = current_dir; - } - - 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; - } - - 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 ); - } + 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 ) { @@ -402,42 +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 ) { @@ -455,9 +398,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } updateOptions( getOptions() ); } - // else if ( o == _write_to_pdf_item ) { - // writeToPdf( _mainpanel.getCurrentPhylogeny() ); final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(), getMainPanel(), _writetopdf_filechooser, @@ -532,43 +473,37 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ); - } - - - } // TODO - // TODO - // TODO - // TODO - // TODO - - - // 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(); - // } + 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(); } @@ -670,19 +605,39 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void init() { _writetopdf_filechooser = new JFileChooser(); + _writetopdf_filechooser.setMultiSelectionEnabled( false ); + _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); _writetographics_filechooser = new JFileChooser(); - final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); + _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 ); @@ -699,7 +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", @@ -744,7 +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; @@ -777,7 +732,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } } - // try { setVisible( false ); setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); @@ -847,11 +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 ); } @@ -882,19 +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" ) ); @@ -943,6 +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() ); @@ -1008,6 +1172,30 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ); @@ -1310,6 +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(); } @@ -1318,6 +1528,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _label_direction_cbmi; } + MainPanel getMainPanel() { + return _mainpanel; + } + Options getOtions() { return _options; } @@ -1414,6 +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; } @@ -1563,6 +1781,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ); } @@ -1596,6 +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 ) { @@ -1637,112 +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 treepanels, final boolean antialias ) {