package org.forester.archaeopteryx;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Container;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
+import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.NoSuchElementException;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.SwingUtilities;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.tools.InferenceManager;
+import org.forester.archaeopteryx.tools.ProcessPool;
+import org.forester.archaeopteryx.tools.ProcessRunning;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.util.ForesterConstants;
public abstract class MainFrame extends JFrame implements ActionListener {
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
- private static final long serialVersionUID = 3655000897845508358L;
- final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 10 );
- static final String TYPE_MENU_HEADER = "Type";
- static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
- static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
- static final String CURVED_TYPE_CBMI_LABEL = "Curved";
- static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
- static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
- static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
- static final String OPTIONS_HEADER = "Options";
- static final String SEARCH_SUBHEADER = "Search:";
- static final String DISPLAY_SUBHEADER = "Display:";
- static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String DISPLAY_SCALE_LABEL = "Display Scale";
- static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
- static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show Overview";
- static final String FONT_SIZE_MENU_LABEL = "Font Size";
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
- static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
- static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
- static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
- static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
- static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
- static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
- JMenuBar _jmenubar;
- JMenu _file_jmenu;
- JMenu _tools_menu;
- JMenu _view_jmenu;
- JMenu _options_jmenu;
- JMenu _font_size_menu;
- JMenu _help_jmenu;
- JMenuItem[] _load_phylogeny_from_webservice_menu_items;
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
+ static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
+ private static final long serialVersionUID = 3655000897845508358L;
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 10 );
+ static final String TYPE_MENU_HEADER = "Type";
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
+ static final String OPTIONS_HEADER = "Options";
+ static final String SEARCH_SUBHEADER = "Search:";
+ static final String DISPLAY_SUBHEADER = "Display:";
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
+ static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
+ static final String DISPLAY_SCALE_LABEL = "Display Scale";
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
+ static final String BG_GRAD_LABEL = "Background Color Gradient";
+ static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
+ static final String SHOW_OVERVIEW_LABEL = "Show Overview";
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
+ static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
+ static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ JMenuBar _jmenubar;
+ JMenu _file_jmenu;
+ JMenu _tools_menu;
+ JMenu _view_jmenu;
+ JMenu _options_jmenu;
+ JMenu _font_size_menu;
+ JMenu _help_jmenu;
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;
// file menu:
- JMenuItem _open_item;
- JMenuItem _open_url_item;
- JMenuItem _save_item;
- JMenuItem _save_all_item;
- JMenuItem _close_item;
- JMenuItem _exit_item;
- JMenuItem _new_item;
+ JMenuItem _open_item;
+ JMenuItem _open_url_item;
+ JMenuItem _save_item;
+ JMenuItem _save_all_item;
+ JMenuItem _close_item;
+ JMenuItem _exit_item;
+ JMenuItem _new_item;
// tools menu:
- JMenuItem _midpoint_root_item;
- JMenuItem _taxcolor_item;
- JMenuItem _confcolor_item;
- JMenuItem _color_rank_jmi;
- JMenuItem _infer_common_sn_names_item;
- JMenuItem _collapse_species_specific_subtrees;
- JMenuItem _collapse_below_threshold; //TODO implememt me
- JMenuItem _obtain_detailed_taxonomic_information_jmi;
- JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
- JMenuItem _obtain_uniprot_seq_information_jmi;
- JMenuItem _move_node_names_to_tax_sn_jmi;
- JMenuItem _move_node_names_to_seq_names_jmi;
- JMenuItem _extract_tax_code_from_node_names_jmi;
+ JMenuItem _midpoint_root_item;
+ JMenuItem _taxcolor_item;
+ JMenuItem _confcolor_item;
+ JMenuItem _color_rank_jmi;
+ JMenuItem _infer_common_sn_names_item;
+ JMenuItem _collapse_species_specific_subtrees;
+ JMenuItem _collapse_below_threshold; //TODO implememt me
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
+ JMenuItem _obtain_uniprot_seq_information_jmi;
+ JMenuItem _move_node_names_to_tax_sn_jmi;
+ JMenuItem _move_node_names_to_seq_names_jmi;
+ JMenuItem _extract_tax_code_from_node_names_jmi;
// font size menu:
- JMenuItem _super_tiny_fonts_item;
- JMenuItem _tiny_fonts_item;
- JMenuItem _small_fonts_item;
- JMenuItem _medium_fonts_item;
- JMenuItem _large_fonts_item;
+ JMenuItem _super_tiny_fonts_item;
+ JMenuItem _tiny_fonts_item;
+ JMenuItem _small_fonts_item;
+ JMenuItem _medium_fonts_item;
+ JMenuItem _large_fonts_item;
// options menu:
// _ screen and print
- JMenuItem _choose_font_mi;
- JMenuItem _switch_colors_mi;
- JCheckBoxMenuItem _label_direction_cbmi;
+ JMenuItem _choose_font_mi;
+ JMenuItem _switch_colors_mi;
+ JCheckBoxMenuItem _label_direction_cbmi;
// _ screen display
- JCheckBoxMenuItem _screen_antialias_cbmi;
- JCheckBoxMenuItem _background_gradient_cbmi;
- JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
- JRadioButtonMenuItem _uniform_cladograms_rbmi;
- JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
- JCheckBoxMenuItem _show_branch_length_values_cbmi;
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
- JCheckBoxMenuItem _show_overview_cbmi;
- JCheckBoxMenuItem _show_domain_labels;
- JCheckBoxMenuItem _abbreviate_scientific_names;
- JCheckBoxMenuItem _color_labels_same_as_parent_branch;
- JMenuItem _overview_placment_mi;
- JMenuItem _choose_minimal_confidence_mi;
- JCheckBoxMenuItem _show_default_node_shapes_cbmi;
- JMenuItem _cycle_node_shape_mi;
- JMenuItem _cycle_node_fill_mi;
- JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
+ JCheckBoxMenuItem _screen_antialias_cbmi;
+ JCheckBoxMenuItem _background_gradient_cbmi;
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
+ JRadioButtonMenuItem _uniform_cladograms_rbmi;
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
+ JCheckBoxMenuItem _show_branch_length_values_cbmi;
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
+ JCheckBoxMenuItem _show_overview_cbmi;
+ JCheckBoxMenuItem _show_domain_labels;
+ JCheckBoxMenuItem _abbreviate_scientific_names;
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;
+ JMenuItem _overview_placment_mi;
+ JMenuItem _choose_minimal_confidence_mi;
+ JCheckBoxMenuItem _show_default_node_shapes_cbmi;
+ JMenuItem _cycle_node_shape_mi;
+ JMenuItem _cycle_node_fill_mi;
+ JMenuItem _choose_node_size_mi;
+ JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;
// _ print
- JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
- JCheckBoxMenuItem _antialias_print_cbmi;
- JCheckBoxMenuItem _print_black_and_white_cbmi;
- JCheckBoxMenuItem _print_using_actual_size_cbmi;
- JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
- JMenuItem _print_size_mi;
- JMenuItem _choose_pdf_width_mi;
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
+ JCheckBoxMenuItem _antialias_print_cbmi;
+ JCheckBoxMenuItem _print_black_and_white_cbmi;
+ JCheckBoxMenuItem _print_using_actual_size_cbmi;
+ JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
+ JMenuItem _print_size_mi;
+ JMenuItem _choose_pdf_width_mi;
// _ parsing
- JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
- JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
- JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
+ JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
+ JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
// _ search
- JCheckBoxMenuItem _search_case_senstive_cbmi;
- JCheckBoxMenuItem _search_whole_words_only_cbmi;
- JCheckBoxMenuItem _inverse_search_result_cbmi;
+ JCheckBoxMenuItem _search_case_senstive_cbmi;
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;
+ JCheckBoxMenuItem _inverse_search_result_cbmi;
// type menu:
- JMenu _type_menu;
- JCheckBoxMenuItem _rectangular_type_cbmi;
- JCheckBoxMenuItem _triangular_type_cbmi;
- JCheckBoxMenuItem _curved_type_cbmi;
- JCheckBoxMenuItem _convex_type_cbmi;
- JCheckBoxMenuItem _euro_type_cbmi;
- JCheckBoxMenuItem _rounded_type_cbmi;
- JCheckBoxMenuItem _unrooted_type_cbmi;
- JCheckBoxMenuItem _circular_type_cbmi;
+ JMenu _type_menu;
+ JCheckBoxMenuItem _rectangular_type_cbmi;
+ JCheckBoxMenuItem _triangular_type_cbmi;
+ JCheckBoxMenuItem _curved_type_cbmi;
+ JCheckBoxMenuItem _convex_type_cbmi;
+ JCheckBoxMenuItem _euro_type_cbmi;
+ JCheckBoxMenuItem _rounded_type_cbmi;
+ JCheckBoxMenuItem _unrooted_type_cbmi;
+ JCheckBoxMenuItem _circular_type_cbmi;
// view as text menu:
- JMenuItem _view_as_NH_item;
- JMenuItem _view_as_NHX_item;
- JMenuItem _view_as_XML_item;
- JMenuItem _view_as_nexus_item;
- JMenuItem _display_basic_information_item;
+ JMenuItem _view_as_NH_item;
+ JMenuItem _view_as_NHX_item;
+ JMenuItem _view_as_XML_item;
+ JMenuItem _view_as_nexus_item;
+ JMenuItem _display_basic_information_item;
// help menu:
- JMenuItem _about_item;
- JMenuItem _help_item;
- JMenuItem _website_item;
- JMenuItem _phyloxml_website_item;
- JMenuItem _phyloxml_ref_item;
- JMenuItem _aptx_ref_item;
+ JMenuItem _about_item;
+ JMenuItem _help_item;
+ JMenuItem _website_item;
+ JMenuItem _phyloxml_website_item;
+ JMenuItem _phyloxml_ref_item;
+ JMenuItem _aptx_ref_item;
+ // process menu:
+ JMenu _process_menu;
// Handy pointers to child components:
- MainPanel _mainpanel;
- Container _contentpane;
- TextFrame _textframe;
- Configuration _configuration;
- JMenuItem _remove_branch_color_item;
- Options _options;
+ MainPanel _mainpanel;
+ Container _contentpane;
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
+ Configuration _configuration;
+ JMenuItem _remove_branch_color_item;
+ Options _options;
+ InferenceManager _inference_manager;
+ final ProcessPool _process_pool;
MainFrame() {
- // Empty constructor.
+ _process_pool = ProcessPool.createInstance();
+ }
+
+ public ProcessPool getProcessPool() {
+ return _process_pool;
}
/**
else if ( o == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
else if ( o == _label_direction_cbmi ) {
updateOptions( getOptions() );
}
}
else if ( o == _website_item ) {
try {
- Util.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
+ AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
else if ( o == _phyloxml_website_item ) {
try {
- Util.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
+ AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
else if ( o == _aptx_ref_item ) {
try {
- Util.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
+ AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
else if ( o == _phyloxml_ref_item ) {
try {
- Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
_jmenubar.add( _help_jmenu );
}
+ public void updateProcessMenu() {
+ // In general Swing is not thread safe.
+ // See "Swing's Threading Policy".
+ SwingUtilities.invokeLater( new Runnable() {
+
+ public void run() {
+ doUpdateProcessMenu();
+ }
+ } );
+ }
+
+ private void doUpdateProcessMenu() {
+ if ( _process_pool.size() > 0 ) {
+ if ( _process_menu == null ) {
+ _process_menu = createMenu( "", getConfiguration() );
+ _process_menu.setForeground( Color.RED );
+ }
+ _process_menu.removeAll();
+ final String text = "processes running: " + _process_pool.size();
+ _process_menu.setText( text );
+ _jmenubar.add( _process_menu );
+ for( int i = 0; i < _process_pool.size(); ++i ) {
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
+ }
+ }
+ else {
+ if ( _process_menu != null ) {
+ _process_menu.removeAll();
+ _jmenubar.remove( _process_menu );
+ }
+ }
+ _jmenubar.validate();
+ _jmenubar.repaint();
+ repaint();
+ }
+
void buildTypeMenu() {
_type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
_type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
}
void close() {
- removeTextFrame();
+ removeAllTextFrames();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
void colorRank() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = Util.getAllPossibleRanks();
+ final String[] ranks = AptxUtil.getAllPossibleRanks();
final String rank = ( String ) JOptionPane
.showInputDialog( this,
"What rank should the colorization be based on",
}
}
- void customizeJMenuItem( final JMenuItem jmi ) {
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
if ( jmi != null ) {
jmi.setFont( MainFrame.menu_font );
if ( !getConfiguration().isUseNativeUI() ) {
}
jmi.addActionListener( this );
}
+ return jmi;
}
void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
return _label_direction_cbmi;
}
- MainPanel getMainPanel() {
+ public MainPanel getMainPanel() {
return _mainpanel;
}
return _jmenubar;
}
- Options getOptions() {
+ public Options getOptions() {
return _options;
}
private void removeBranchColors() {
if ( getMainPanel().getCurrentPhylogeny() != null ) {
- Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
}
}
- void removeTextFrame() {
- if ( _textframe != null ) {
- _textframe.close();
- _textframe = null;
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
+ }
+ else {
+ _textframes.removeFirst();
+ }
+ }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
+ }
+ }
+ }
+
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
}
+ _textframes.clear();
}
void setConfiguration( final Configuration configuration ) {
_options = options;
}
+ void setInferenceManager( final InferenceManager i ) {
+ _inference_manager = i;
+ }
+
+ public InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
setTypeMenuToAllUnselected();
switch ( type ) {
}
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+ && _show_confidence_stddev_cbmi.isSelected() );
if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
}
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
&& ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ }
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ }
+ else {
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ }
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
&& _print_black_and_white_cbmi.isSelected() );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
}
void displayBasicInformation() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
- return;
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
}
- _textframe = TextFrame.instantiate( Util.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
}
void viewAsNexus() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Nexus";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
+ title );
}
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() );
}
void viewAsNH() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "New Hampshire";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny()
+ .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+ title );
}
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) );
}
void viewAsNHX() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "NHX";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
}
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
}
void viewAsXML() {
- removeTextFrame();
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
- && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "phyloXML";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
}
}
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
/**
* Display the about box.
*/
static void about() {
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
- about.append( "Copyright (C) 2007-2011 Christian Zmasek\n" );
+ about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
about.append( "All Rights Reserved\n" );
about.append( "License: GNU Lesser General Public License (LGPL)\n" );
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
}
}
- static void help( final Map<String, WebLink> weblinks ) {
+ void help( final Map<String, WebLink> weblinks ) {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
sb.append( "-------------------\n" );
sb.append( "\n" );
sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString() );
+ TextFrame.instantiate( sb.toString(), "Help", _textframes );
}
static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
mi.setEnabled( true );
}
- else if ( ForesterUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
mi.setEnabled( true );
}
else {
git://source.jalview.org / jalview.git / blobdiff