// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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 java.util.Set;
+import javax.swing.Box;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JFrame;
+import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTextField;
+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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
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";
- 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_EXT = "Show External Node Shapes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal 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";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Show Basic Tree Information";
+ 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;
+ // Analysis menu
+ JMenu _analysis_menu;
+ JMenuItem _load_species_tree_item;
+ JMenuItem _gsdi_item;
+ JMenuItem _gsdir_item;
+ JMenuItem _lineage_inference;
+ JMenuItem _function_analysis;
// 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 _infer_common_sn_names_item;
- JMenuItem _collapse_species_specific_subtrees;
- JMenuItem _collapse_below_threshold; //TODO implememt me
- JMenuItem _obtain_detailed_taxonomic_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 _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_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 _annotate_item;
// 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;
- 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_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 _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_internal_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_external_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;
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
+ 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 _view_as_NH_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;
+ private Phylogeny _species_tree;
+ InferenceManager _inference_manager;
+ final ProcessPool _process_pool;
+ private String _previous_node_annotation_ref;
MainFrame() {
- // Empty constructor.
+ _process_pool = ProcessPool.createInstance();
}
/**
* Action performed.
*/
+ @Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
boolean is_applet = false;
else if ( o == _exit_item ) {
close();
}
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _taxcolor_item ) {
taxColor();
}
else if ( o == _confcolor_item ) {
confColor();
}
- else if ( o == _infer_common_sn_names_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().inferCommonPartOfScientificNames();
- }
+ else if ( o == _color_rank_jmi ) {
+ colorRank();
}
else if ( o == _collapse_species_specific_subtrees ) {
if ( isSubtreeDisplayed() ) {
}
midpointRoot();
}
+ else if ( o == _annotate_item ) {
+ annotateSequences();
+ }
else if ( o == _switch_colors_mi ) {
switchColors();
}
+ else if ( o == _display_basic_information_item ) {
+ displayBasicInformation();
+ }
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
- else if ( o == _view_as_NHX_item ) {
- viewAsNHX();
- }
else if ( o == _view_as_XML_item ) {
viewAsXML();
}
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_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_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() );
}
about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ help();
}
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() );
_contentpane.repaint();
}
- boolean isSubtreeDisplayed() {
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
- JOptionPane
- .showMessageDialog( this,
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
- "Operation can not be exectuted on a sub-tree",
- JOptionPane.WARNING_MESSAGE );
- return true;
- }
- return false;
+ public Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ /**
+ * This method returns the current external node data which
+ * 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() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ public InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ public ProcessPool getProcessPool() {
+ return _process_pool;
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ public void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
+ public void updateProcessMenu() {
+ // In general Swing is not thread safe.
+ // See "Swing's Threading Policy".
+ SwingUtilities.invokeLater( new Runnable() {
+
+ @Override
+ public void run() {
+ doUpdateProcessMenu();
+ }
+ } );
}
void activateSaveAllIfNeeded() {
}
void buildViewMenu() {
- _view_jmenu = createMenu( "View as Text", getConfiguration() );
+ _view_jmenu = createMenu( "View", getConfiguration() );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ _view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
- customizeJMenuItem( _view_as_NHX_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _view_as_nexus_item );
_jmenubar.add( _view_jmenu );
}
- 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 enter 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 );
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
}
- catch ( final Exception ex ) {
- success = false;
+ else {
+ _textframes.removeFirst();
}
}
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
}
}
}
void close() {
- removeTextFrame();
+ removeAllTextFrames();
if ( _mainpanel != null ) {
_mainpanel.terminate();
}
dispose();
}
+ 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 confColor() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().confColor();
}
}
- 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 ) {
}
}
+ void displayBasicInformation() {
+ 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 );
+ }
+ }
+
void exceptionOccuredDuringOpenFile( final Exception e ) {
try {
_mainpanel.getCurrentTreePanel().setArrowCursor();
JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
}
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
JOptionPane.showMessageDialog( this,
}
}
- Configuration getConfiguration() {
- return _configuration;
- }
-
TreePanel getCurrentTreePanel() {
return getMainPanel().getCurrentTreePanel();
}
return _label_direction_cbmi;
}
- MainPanel getMainPanel() {
- return _mainpanel;
- }
-
JMenuBar getMenuBarOfMainFrame() {
return _jmenubar;
}
- Options getOptions() {
- return _options;
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ void help() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( "Display options\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
+ sb.append( "Clickable tree nodes\n" );
+ sb.append( "--------------------\n" );
+ sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
+ sb.append( "or by right clicking:\n" );
+ sb.append( "o Display Node Data -- display information for a node\n" );
+ sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
+ sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
+ sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
+ sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
+ sb.append( "o Colorize Subtree -- color a subtree\n" );
+ sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
+ sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
+ sb.append( "- there may be additional choices depending on this particular setup\n\n" );
+ sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
+ sb.append( "Zooming\n" );
+ sb.append( "---------\n" );
+ sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
+ sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
+ sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
+ sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
+ sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
+ sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
+ sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
+ sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
+ sb.append( "Quick tree manipulation:\n" );
+ sb.append( "------------------------\n" );
+ sb.append( "Order Subtrees -- order the tree by branch length\n" );
+ sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
+ sb.append( "Memory problems (Java heap space error)\n" );
+ sb.append( "---------------------------------------\n" );
+ sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
+ sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
+ sb.append( "the '-Xmx' Java command line option. For example:\n" );
+ sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
+ // + "General remarks\n"
+ // + "---------------\n"
+ // +
+ // "o The application version permits copying to the clipboard \n"
+ // +
+ // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
+ // +
+ // "o Changes made to a subtree affect this subtree and its subtrees,\n"
+ // + " but not any of its parent tree(s).\n"
+ // +
+ // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
+ // +
+ // " are likely to be bootstrap values instead of branch length values.\n\n"
+ // +
+ // " Remarks regarding SDI (Speciation Duplication Inference):\n"
+ // +
+ // "o Each external node of the gene tree (in display) needs to be associated with\n"
+ // +
+ // " a species: either directly through the \"Species\" field, or the species\n"
+ // +
+ // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
+ // +
+ // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
+ // +
+ // "o A species tree for each species of the gene tree needs to be loaded with\n"
+ // +
+ // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
+ // +
+ // "o !External nodes of the gene tree associated with species not present in\n"
+ // +
+ // " the species tree are REMOVED prior to SDI execution!\n"
+ // +
+ // "o Both the gene tree and the species tree must be completely binary.\n"
+ // +
+ // "o Duplications and speciations are a function of the position of the root.\n"
+ // +
+ // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
+ // + " incorrect and need to be inferred again\n"
+ // +
+ // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
+ sb.append( "phyloXML\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
+ sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
+ sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
+ sb.append( "\n" );
+ sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
+ sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
+ TextFrame.instantiate( sb.toString(), "Help", _textframes );
}
void initializeTypeMenu( final Options options ) {
}
}
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
+ }
+ }
+ return false;
+ }
+
void midpointRoot() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().midpointRoot();
new Thread( reader ).start();
}
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- void removeTextFrame() {
- if ( _textframe != null ) {
- _textframe.close();
- _textframe = null;
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
}
+ _textframes.clear();
}
void setConfiguration( final Configuration configuration ) {
_configuration = configuration;
}
+ void setInferenceManager( final InferenceManager i ) {
+ _inference_manager = i;
+ }
+
void setOptions( final Options options ) {
_options = options;
}
}
}
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );
_circular_type_cbmi.setSelected( false );
}
- void showWhole() {
- _mainpanel.getControlPanel().showWhole();
- }
-
void switchColors() {
final TreeColorSet colorset = _mainpanel.getTreeColorSet();
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
&& _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.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_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 )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
- && _extract_pfam_style_tax_codes_cbmi.isSelected() );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
}
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;
+ void viewAsXML() {
+ 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 );
}
- _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 ) );
+ private void annotateSequences() {
+ if ( getCurrentTreePanel() != null ) {
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "Need to select nodes, either via direct selection or via the \"Search\" function",
+ "No nodes selected for annotation",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final JTextField ref_field = new JTextField( 10 );
+ final JTextField desc_filed = new JTextField( 20 );
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
+ : getPreviousNodeAnnotationReference() );
+ final JPanel my_panel = new JPanel();
+ my_panel.add( new JLabel( "Reference " ) );
+ my_panel.add( ref_field );
+ my_panel.add( Box.createHorizontalStrut( 15 ) );
+ my_panel.add( new JLabel( "Description " ) );
+ my_panel.add( desc_filed );
+ final int result = JOptionPane.showConfirmDialog( null,
+ my_panel,
+ "Enter the sequence annotation(s) for the "
+ + nodes.size() + " selected nodes",
+ JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ String ref = ref_field.getText();
+ String desc = desc_filed.getText();
+ if ( !ForesterUtil.isEmpty( ref ) ) {
+ ref = ref.trim();
+ ref = ref.replaceAll( "\\s+", " " );
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
+ || ( ref.length() < 3 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Reference needs to be in the form of \"GO:1234567\"",
+ "Illegal Format for Annotation Reference",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ }
+ if ( ref != null ) {
+ setPreviousNodeAnnotationReference( ref );
+ }
+ if ( desc != null ) {
+ desc = desc.trim();
+ desc = desc.replaceAll( "\\s+", " " );
+ }
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
+ for( final Long id : nodes ) {
+ final PhylogenyNode n = phy.getNode( id );
+ ForesterUtil.ensurePresenceOfSequence( n );
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
+ : new Annotation( ref );
+ if ( !ForesterUtil.isEmpty( desc ) ) {
+ ann.setDesc( desc );
+ }
+ n.getNodeData().getSequence().addAnnotation( ann );
+ }
+ }
+ getMainPanel().getControlPanel().showAnnotations();
+ }
+ }
}
}
+ 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 enter 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 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();
+ }
+
+ private String getPreviousNodeAnnotationReference() {
+ return _previous_node_annotation_ref;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+ _previous_node_annotation_ref = previous_node_annotation_ref;
+ }
+
/**
* 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) 2013 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 ) ) {
JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
}
+ 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 );
+ }
+ }
+ }
+ }
+
static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
}
return label;
}
+ 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 cycleOverview( final Options op, final TreePanel tree_panel ) {
switch ( op.getOvPlacement() ) {
case LOWER_LEFT:
default:
throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
}
- tree_panel.updateOvSettings();
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
+ }
}
- static void help( final Map<String, WebLink> weblinks ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
+ 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..." );
}
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\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() );
}
- 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 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( "Overview Placement..." );
+ mi.setText( "Cycle Node Shape Fill Type..." );
+ }
+ }
+
+ 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( "Cycle Overview Placement..." );
}
}
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