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;
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"
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;
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;
private ButtonGroup _radio_group_1;
private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
private JMenuItem _cycle_node_shape_mi;
private JMenuItem _cycle_node_fill_mi;
private JMenuItem _choose_node_size_mi;
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 ) {
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() );
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();
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 == _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 ) {
}
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();
}
* 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() {
/**
* 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
}
/**
- * 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
@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 );
}
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",
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;
}
}
}
- //
try {
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
_jmenubar = new JMenuBar();
if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+ buildFileMenu();
if ( !getConfiguration().isUseNativeUI() ) {
_jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
}
@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() );
}
}
} );
.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 );
}
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" ) );
.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() );
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
- /////
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
_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_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( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
}
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
_options_jmenu
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
- /////
_options_jmenu.addSeparator();
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
_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 );
.isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
.isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+ .isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
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() );
}
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() {
- if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
+ && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
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();
}
return _label_direction_cbmi;
}
+ MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
Options getOtions() {
return _options;
}
_configuration = configuration;
}
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
void setOptions( final Options options ) {
_options = options;
}
&& _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 );
}
&& _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 );
}
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 ) {
}
}
- 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() );
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
+ + o.getPrintSizeY() + ")" );
}
- 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;
- }
-
- 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 ) {
git://source.jalview.org / jalview.git / blobdiff