}
else if ( o == _help_item ) {
try {
- AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
+ AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _website_item ) {
try {
- AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
+ AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_website_item ) {
try {
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _aptx_ref_item ) {
try {
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
+ AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_ref_item ) {
try {
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _color_by_taxonomic_group_cbmi ) {
e.printStackTrace();
// Do nothing. Not important.
}
- final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+ final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
final Configuration configuration = new Configuration( config_filename, true, true, true );
setConfiguration( configuration );
setOptions( Options.createInstance( configuration ) );
setupUI();
- final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ final String tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
if ( ForesterUtil.isEmpty( tree_url_str ) ) {
ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
- + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
- + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
return;
}
AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
ForesterUtil.printErrorMessage( NAME, "error: " + e );
e.printStackTrace();
JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
- + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+ + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
}
if ( phys_url == null ) {
ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
- + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
JOptionPane.showMessageDialog( this,
NAME + ": Could not create URL from: \"" + tree_url_str,
"Failed to create URL",
AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
}
//
- final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
+ final String species_tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
Phylogeny[] species_trees = null;
}
catch ( final IOException e ) {
ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
- + "]" );
+ + "]" );
JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
+ species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
}
}
}
}
- //
try {
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
public void componentResized( final ComponentEvent e ) {
if ( getMainPanel().getCurrentTreePanel() != null ) {
getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
- .getCurrentTreePanel()
- .getWidth(),
+ .getCurrentTreePanel()
+ .getWidth(),
getMainPanel()
- .getCurrentTreePanel()
- .getHeight() );
+ .getCurrentTreePanel()
+ .getHeight() );
}
}
} );
AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
if ( getSpeciesTree() != null ) {
AptxUtil.printAppletMessage( NAME,
- "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
}
AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
.getRelevantSequenceRelationTypes() ) {
getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
}
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
if ( default_relation != null ) {
getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
}
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
if ( default_sequence != null ) {
getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
}
.showInputDialog( this,
"Please the minimum for confidence values to be displayed.\n" + "[current value: "
+ getOptions().getMinConfidenceValue() + "]\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getMinConfidenceValue() );
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
if ( !ForesterUtil.isEmpty( s ) ) {
boolean success = true;
double m = 0.0;
"Please enter the default line width for PDF export.\n"
+ "[current value: "
+ getOptions().getPrintLineWidth() + "]\n",
- "Line Width for PDF Export",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getPrintLineWidth() );
+ "Line Width for PDF Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintLineWidth() );
if ( !ForesterUtil.isEmpty( s ) ) {
boolean success = true;
float f = 0.0f;
+ "[current values: "
+ getOptions().getPrintSizeX() + ", "
+ getOptions().getPrintSizeY() + "]\n"
- + "[A4: " + Constants.A4_SIZE_X + ", "
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "
- + Constants.US_LETTER_SIZE_X + ", "
- + Constants.US_LETTER_SIZE_Y + "]",
- "Default Size for Graphics Export",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getPrintSizeX() + ", "
- + getOptions().getPrintSizeY() );
+ + "[A4: " + AptxConstants.A4_SIZE_X + ", "
+ + AptxConstants.A4_SIZE_Y + "]\n" + "[US Letter: "
+ + AptxConstants.US_LETTER_SIZE_X + ", "
+ + AptxConstants.US_LETTER_SIZE_Y + "]",
+ "Default Size for Graphics Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintSizeX() + ", "
+ + getOptions().getPrintSizeY() );
if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
boolean success = true;
int x = 0;
_analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
customizeJMenuItem( _gsdi_item );
customizeJMenuItem( _gsdir_item );
- // _analysis_menu.addSeparator();
- // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
- // customizeJMenuItem( _lineage_inference );
- // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _analysis_menu.addSeparator();
_jmenubar.add( _analysis_menu );
}
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu
- .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
+ .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
_radio_group_1 = new ButtonGroup();
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
_options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
_options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
_options_jmenu
- .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu
- .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
+ .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
+ .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
_options_jmenu
- .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
+ .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
//
_options_jmenu.addSeparator();
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
_options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
_options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
_options_jmenu
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
_options_jmenu
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
_options_jmenu
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
//
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
- .isGraphicsExportUsingActualSize() );
+ .isGraphicsExportUsingActualSize() );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
//
customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
+ .isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
+ .isShowDefaultNodeShapesInternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
- .isShowDefaultNodeShapesForMarkedNodes() );
+ .isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
_tools_menu.addSeparator();
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
_remove_visual_styles_item
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
customizeJMenuItem( _remove_visual_styles_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
_remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
void buildViewMenu() {
_view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
_view_jmenu
- .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ 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 );
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
+ 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 );
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
+ 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 );
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
+ 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 );
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
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 );
+ .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;
}
}
void updateOptions( final Options options ) {
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
- && _background_gradient_cbmi.isSelected() );
+ && _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
- && _show_annotation_ref_source.isSelected() );
+ && _show_annotation_ref_source.isSelected() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
- && _abbreviate_scientific_names.isSelected() );
+ && _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
- && _color_labels_same_as_parent_branch.isSelected() );
+ && _color_labels_same_as_parent_branch.isSelected() );
options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
- && _show_default_node_shapes_internal_cbmi.isSelected() );
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
- && _show_default_node_shapes_external_cbmi.isSelected() );
+ && _show_default_node_shapes_external_cbmi.isSelected() );
options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
- && _search_case_senstive_cbmi.isSelected() );
+ && _search_case_senstive_cbmi.isSelected() );
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
options.setShowScale( _show_scale_cbmi.isSelected() );
}
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
- && _show_confidence_stddev_cbmi.isSelected() );
+ && _show_confidence_stddev_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
- && _search_whole_words_only_cbmi.isSelected() );
+ && _search_whole_words_only_cbmi.isSelected() );
options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
- && _inverse_search_result_cbmi.isSelected() );
+ && _inverse_search_result_cbmi.isSelected() );
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
- && ( _print_using_actual_size_cbmi.isSelected() ) );
+ && ( _print_using_actual_size_cbmi.isSelected() ) );
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
- && _print_black_and_white_cbmi.isSelected() );
+ && _print_black_and_white_cbmi.isSelected() );
if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
- .getNhConversionSupportValueStyle() ),
- title );
+ .getNhConversionSupportValueStyle() ),
+ title );
}
}
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
- .getNhConversionSupportValueStyle() ),
- title );
+ .getNhConversionSupportValueStyle() ),
+ title );
}
}
git://source.jalview.org / jalview.git / blobdiff