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 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;
import org.forester.util.ForesterUtil;
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 Boxes";
- 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 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;
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 _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;
// _ screen display
JCheckBoxMenuItem _screen_antialias_cbmi;
JCheckBoxMenuItem _background_gradient_cbmi;
- JCheckBoxMenuItem _show_node_boxes_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_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 _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;
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;
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 == _confcolor_item ) {
confColor();
}
+ else if ( o == _color_rank_jmi ) {
+ colorRank();
+ }
else if ( o == _infer_common_sn_names_item ) {
if ( isSubtreeDisplayed() ) {
return;
else if ( o == _choose_minimal_confidence_mi ) {
chooseMinimalConfidence();
}
+ else if ( o == _choose_node_size_mi ) {
+ chooseNodeSize( getOptions(), this );
+ }
else if ( o == _overview_placment_mi ) {
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
}
+ else if ( o == _cycle_node_fill_mi ) {
+ MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+ }
+ else if ( o == _cycle_node_shape_mi ) {
+ MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+ }
else if ( o == _screen_antialias_cbmi ) {
updateOptions( getOptions() );
updateScreenTextAntialias( getMainPanel().getTreePanels() );
else if ( o == _color_labels_same_as_parent_branch ) {
updateOptions( getOptions() );
}
- else if ( o == _show_node_boxes_cbmi ) {
+ else if ( o == _show_default_node_shapes_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
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 ) );
}
}
+ static void chooseNodeSize( final Options options, final Component parent ) {
+ final String s = ( String ) JOptionPane.showInputDialog( parent,
+ "Please enter the default size for node shapes.\n"
+ + "[current value: "
+ + options.getDefaultNodeShapeSize() + "]\n",
+ "Node Shape Size",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ options.getDefaultNodeShapeSize() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ final short size = ForesterUtil.roundToShort( m );
+ if ( size >= 0.0 ) {
+ options.setDefaultNodeShapeSize( size );
+ }
+ }
+ }
+ }
+
void close() {
removeTextFrame();
if ( _mainpanel != null ) {
}
}
+ void colorRank() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ final String[] ranks = AptxUtil.getAllPossibleRanks();
+ final String rank = ( String ) JOptionPane
+ .showInputDialog( this,
+ "What rank should the colorization be based on",
+ "Rank Selection",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ ranks,
+ null );
+ if ( !ForesterUtil.isEmpty( rank ) ) {
+ _mainpanel.getCurrentTreePanel().colorRank( rank );
+ }
+ }
+ }
+
void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
if ( item != null ) {
item.setFont( MainFrame.menu_font );
}
}
- 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() );
}
}
_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 ) {
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
- options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
+ options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
+ && _show_default_node_shapes_cbmi.isSelected() );
+ options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
+ && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
}
}
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 )
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
return;
}
- _textframe = TextFrame.instantiate( Util.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
+ _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
}
void viewAsNexus() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
+ || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
return;
}
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() );
+ _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
+ .getNhConversionSupportValueStyle() ) );
}
void viewAsNH() {
removeTextFrame();
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
- || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
+ || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) {
return;
}
- _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) );
+ _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
+ .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
}
void viewAsNHX() {
*/
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 ) ) {
default:
throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
}
- tree_panel.updateOvSettings();
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
+ }
+ }
+
+ static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getDefaultNodeFill() ) {
+ case GRADIENT:
+ op.setDefaultNodeFill( NodeFill.SOLID );
+ break;
+ case NONE:
+ op.setDefaultNodeFill( NodeFill.GRADIENT );
+ break;
+ case SOLID:
+ op.setDefaultNodeFill( NodeFill.NONE );
+ break;
+ default:
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
+ }
+ }
+
+ static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getDefaultNodeShape() ) {
+ case CIRCLE:
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );
+ break;
+ case RECTANGLE:
+ op.setDefaultNodeShape( NodeShape.CIRCLE );
+ break;
+ default:
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
+ }
}
static void help( final Map<String, WebLink> weblinks ) {
TextFrame.instantiate( sb.toString() );
}
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
- mi.setText( "Overview Placement... (current: " + tree_panel.getOptions().getOvPlacement() + ")" );
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
}
else {
- mi.setText( "Overview Placement..." );
+ mi.setText( "Cycle Overview Placement..." );
+ }
+ }
+
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
+ mi.setText( "Cycle Node Shape Fill Type... (current: "
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Node Shape Fill Type..." );
}
}
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 {
mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
}
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
+ }
+
static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
final JCheckBoxMenuItem scale,
final JCheckBoxMenuItem branch_lengths,
git://source.jalview.org / jalview.git / blobdiff