import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
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";
+ 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 _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;
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;
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;
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() );
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",
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.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.crateBasicInformation( _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() {
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