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 "
}
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() );
}
.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;
+ 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() );
+ "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 );
}
}
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9907 experimental";
- final static String PRG_DATE = "150311";
+ final static String VERSION = "0.9908 experimental";
+ final static String PRG_DATE = "150312";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
- "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
+ "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
final static boolean VERBOSE_DEFAULT = false;
final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100;
final static String AUTHOR_EMAIL = "phyloxml@gmail.com";
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.ProcessPool;\r
import org.forester.archaeopteryx.tools.ProcessRunning;\r
static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
JMenuBar _jmenubar;\r
JMenu _file_jmenu;\r
JMenu _tools_menu;\r
else if ( o == _choose_pdf_width_mi ) {\r
choosePdfWidth();\r
}\r
+ else if ( o == _lineage_inference ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Subtree is shown.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ executeLineageInference();\r
+ }\r
else {\r
if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
my_panel,\r
"Enter the sequence annotation(s) for the "\r
+ nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
+ JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
String ref = ref_field.getText();\r
String desc = desc_filed.getText();\r
for( final PhylogenyNode n : nodes ) {\r
ForesterUtil.ensurePresenceOfSequence( n );\r
final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
+ : new Annotation( ref );\r
if ( !ForesterUtil.isEmpty( desc ) ) {\r
ann.setDesc( desc );\r
}\r
.showInputDialog( this,\r
"Please enter the minimum for confidence values to be displayed.\n"\r
+ "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final int todo = nodes.size();\r
return;\r
}\r
final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
if ( !delete ) {\r
final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
"Please enter the default line width for PDF export.\n"\r
+ "[current value: "\r
+ getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
float f = 0.0f;\r
+ Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ Constants.US_LETTER_SIZE_X + ", "\r
+ Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
boolean success = true;\r
int x = 0;\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
}\r
\r
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
if ( getCurrentTreePanel() != null ) {\r
if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
return true;\r
}\r
}\r
void updateOptions( final Options options ) {\r
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
+ && _background_gradient_cbmi.isSelected() );\r
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
+ && _show_annotation_ref_source.isSelected() );\r
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
+ && _abbreviate_scientific_names.isSelected() );\r
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
}\r
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
+ && _search_case_senstive_cbmi.isSelected() );\r
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
options.setShowScale( _show_scale_cbmi.isSelected() );\r
}\r
}\r
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
&& _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
+ && _print_black_and_white_cbmi.isSelected() );\r
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
}\r
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
+ && _replace_underscores_cbmi.isSelected() );\r
options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
+ && _inverse_search_result_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi != null ) {\r
options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
}\r
showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
}\r
}\r
\r
"Please enter the default size for node shapes.\n"\r
+ "[current value: "\r
+ options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to PDF file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
if ( !opts.isPrintUsingActualSize() ) {\r
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
+ + ")" );\r
}\r
else {\r
mi.setText( "Select Color Scheme..." );\r
JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to an image file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
contentpane.repaint();\r
}
// build the menu bar
_jmenubar = new JMenuBar();
+ buildFileMenu();
if ( !_configuration.isUseNativeUI() ) {
_jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
}
- if ( getSpeciesTree() != null ) {
- buildAnalysisMenu();
- }
- buildFileMenu();
+ buildAnalysisMenu();
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
- _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" );
+ if ( getSpeciesTree() != null ) {
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _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" );
_jmenubar.add( _analysis_menu );
}
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
-import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;\r
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;\r
\r
public final class MainFrameApplication extends MainFrame {\r
\r
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
- private final static int FRAME_X_SIZE = 800;\r
- private final static int FRAME_Y_SIZE = 800;\r
+ private final static int FRAME_X_SIZE = 800;\r
+ private final static int FRAME_Y_SIZE = 800;\r
// Filters for the file-open dialog (classes defined in this file)\r
- private static final long serialVersionUID = -799735726778865234L;\r
- private static final boolean PREPROCESS_TREES = false;\r
+ private static final long serialVersionUID = -799735726778865234L;\r
+ private static final boolean PREPROCESS_TREES = false;\r
private final JFileChooser _values_filechooser;\r
private final JFileChooser _sequences_filechooser;\r
private final JFileChooser _open_filechooser;\r
private ButtonGroup _radio_group_1;\r
private ButtonGroup _radio_group_2;\r
// Others:\r
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
- double _min_not_collapse_bl = 0.001;\r
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
private JMenu _inference_menu;\r
private JMenuItem _inference_from_msa_item;\r
private JMenuItem _inference_from_seqs_item;\r
// Phylogeny Inference\r
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
- private Msa _msa = null;\r
- private File _msa_file = null;\r
- private List<MolecularSequence> _seqs = null;\r
- private File _seqs_file = null;\r
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
+ private Msa _msa = null;\r
+ private File _msa_file = null;\r
+ private List<MolecularSequence> _seqs = null;\r
+ private File _seqs_file = null;\r
JMenuItem _read_values_jmi;\r
JMenuItem _read_seqs_jmi;\r
\r
public void componentResized( final ComponentEvent e ) {\r
if ( _mainpanel.getCurrentTreePanel() != null ) {\r
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
- .getWidth(),\r
+ .getWidth(),\r
_mainpanel.getCurrentTreePanel()\r
- .getHeight() );\r
+ .getHeight() );\r
}\r
}\r
} );\r
else if ( o == _load_species_tree_item ) {\r
readSpeciesTreeFromFile();\r
}\r
- else if ( o == _lineage_inference ) {\r
- if ( isSubtreeDisplayed() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Subtree is shown.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- executeLineageInference();\r
- }\r
else if ( o == _obtain_detailed_taxonomic_information_jmi ) {\r
if ( isSubtreeDisplayed() ) {\r
return;\r
JOptionPane.showMessageDialog( this,\r
"Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
int not_found = 0;\r
}\r
catch ( final IllegalArgumentException e ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
if ( row < 0 ) {\r
catch ( final NumberFormatException e ) {\r
JOptionPane.showMessageDialog( this,\r
"Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
+ + "\" into a decimal value",\r
"Issue with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
if ( !l.isEmpty() ) {\r
if ( node.getNodeData().getProperties() != null ) {\r
node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
}\r
node.getNodeData().setVector( l );\r
}\r
}\r
if ( not_found > 0 ) {\r
JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
}\r
getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
if ( nodes.size() > 1 ) {\r
JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
setArrowCursor();\r
return;\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
}\r
}\r
if ( to_be_removed.size() > 0 ) {\r
JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
}\r
if ( to_be_removed.size() > 0 ) {\r
JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
if ( getMsa() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
if ( getSeqs() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
}\r
JOptionPane.showMessageDialog( this,\r
"Extracted taxonomic data from " + all + counter\r
- + " named external nodes:\n" + sb.toString() + failed,\r
+ + " named external nodes:\n" + sb.toString() + failed,\r
"Taxonomic Data Extraction Completed",\r
counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
: JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
- + "or nodes already have taxonomic data?\n",\r
+ .showMessageDialog( this,\r
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
+ + "or nodes already have taxonomic data?\n",\r
"No Taxonomic Data Extracted",\r
JOptionPane.ERROR_MESSAGE );\r
}\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
if ( ( phy != null ) && !phy.isEmpty() ) {\r
PhylogenyMethods\r
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
}\r
}\r
}\r
if ( getMainPanel().getMainFrame() == null ) {\r
// Must be "E" applet version.\r
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
else {\r
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
try {\r
final PhylogenyParser parser = ParserUtils\r
.createParserDependingOnFileType( file, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
setSpecialOptionsForNexParser( nex );\r
_mainpanel.getControlPanel().showWhole();\r
if ( nhx_or_nexus && one_desc ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "One or more trees contain (a) node(s) with one descendant, "\r
- + ForesterUtil.LINE_SEPARATOR\r
- + "possibly indicating illegal parentheses within node names.",\r
+ .showMessageDialog( this,\r
+ "One or more trees contain (a) node(s) with one descendant, "\r
+ + ForesterUtil.LINE_SEPARATOR\r
+ + "possibly indicating illegal parentheses within node names.",\r
"Warning: Possible Error in New Hampshire Formatted Data",\r
JOptionPane.WARNING_MESSAGE );\r
}\r
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
+ .createPhyloXmlParserXsdValidating(), file );\r
t = trees[ 0 ];\r
}\r
catch ( final Exception e ) {\r
else {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
+ .createPhyloXmlParserXsdValidating(), file );\r
t = trees[ 0 ];\r
}\r
catch ( final Exception e ) {\r
exception = true;\r
t = null;\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Species tree contains external node(s) without taxonomy information",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Species tree contains external node(s) without taxonomy information",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
break;\r
}\r
else {\r
"Taxonomy ["\r
+ node.getNodeData().getTaxonomy().asSimpleText()\r
+ "] is not unique in species tree",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
break;\r
}\r
else {\r
_file_jmenu.addSeparator();\r
final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
- .getAvailablePhylogeniesWebserviceClients().size() ];\r
+ .getAvailablePhylogeniesWebserviceClients().size() ];\r
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
_load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
customizeJMenuItem( _open_item );\r
_open_item\r
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
customizeJMenuItem( _open_url_item );\r
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
MainFrame\r
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
} );\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
_options_jmenu\r
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
_options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
_radio_group_1 = new ButtonGroup();\r
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
_options_jmenu\r
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
_options_jmenu\r
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
_options_jmenu\r
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
_options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
_options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
_options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
_options_jmenu\r
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
_options_jmenu\r
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
_options_jmenu\r
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
_options_jmenu\r
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
_options_jmenu\r
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
_options_jmenu\r
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
_options_jmenu\r
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
_options_jmenu\r
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
_extract_taxonomy_pfam_strict_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
_extract_taxonomy_pfam_relaxed_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
_extract_taxonomy_agressive_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
_radio_group_2 = new ButtonGroup();\r
_radio_group_2.add( _extract_taxonomy_no_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
_options_jmenu\r
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
_use_brackets_for_conf_in_nh_export_cbmi\r
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
_options_jmenu\r
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
customizeJMenuItem( _choose_font_mi );\r
customizeJMenuItem( _choose_minimal_confidence_mi );\r
customizeJMenuItem( _switch_colors_mi );\r
customizeJMenuItem( _choose_pdf_width_mi );\r
customizeJMenuItem( _overview_placment_mi );\r
customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
- .isShowDefaultNodeShapesExternal() );\r
+ .isShowDefaultNodeShapesExternal() );\r
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
- .isShowDefaultNodeShapesInternal() );\r
+ .isShowDefaultNodeShapesInternal() );\r
customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
- .isShowDefaultNodeShapesForMarkedNodes() );\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
customizeJMenuItem( _cycle_node_shape_mi );\r
customizeJMenuItem( _cycle_node_fill_mi );\r
customizeJMenuItem( _choose_node_size_mi );\r
customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
- .isInternalNumberAreConfidenceForNhParsing() );\r
+ .isInternalNumberAreConfidenceForNhParsing() );\r
customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
- .isReplaceUnderscoresInNhParsing() );\r
+ .isReplaceUnderscoresInNhParsing() );\r
customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
- .isGraphicsExportUsingActualSize() );\r
+ .isGraphicsExportUsingActualSize() );\r
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
_jmenubar.add( _options_jmenu );\r
_inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
customizeJMenuItem( _inference_from_seqs_item );\r
_inference_from_seqs_item\r
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
}\r
else {\r
_inference_menu\r
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
customizeJMenuItem( _inference_from_seqs_item );\r
_inference_from_seqs_item.setEnabled( false );\r
}\r
_tools_menu.addSeparator();\r
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
_remove_visual_styles_item\r
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
customizeJMenuItem( _remove_visual_styles_item );\r
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
_remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
customizeJMenuItem( _collapse_species_specific_subtrees );\r
_collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
_tools_menu\r
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
customizeJMenuItem( _collapse_below_threshold );\r
_collapse_below_threshold\r
- .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
//\r
_tools_menu\r
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
customizeJMenuItem( _collapse_below_branch_length );\r
_collapse_below_branch_length\r
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
//\r
_tools_menu.addSeparator();\r
_tools_menu\r
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
_extract_tax_code_from_node_names_jmi\r
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
_tools_menu\r
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
_move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
_tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
customizeJMenuItem( _obtain_seq_information_jmi );\r
_obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
_tools_menu\r
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
_obtain_detailed_taxonomic_information_jmi\r
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
_tools_menu\r
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
_obtain_detailed_taxonomic_information_deleting_jmi\r
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
_tools_menu.addSeparator();\r
_tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
customizeJMenuItem( _read_values_jmi );\r
_tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
customizeJMenuItem( _read_seqs_jmi );\r
_read_seqs_jmi\r
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
_jmenubar.add( _tools_menu );\r
}\r
\r
exit();\r
}\r
\r
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
void exit() {\r
removeAllTextFrames();\r
_mainpanel.terminate();\r
}\r
else {\r
parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
}\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
nhx_or_nexus = true;\r
JOptionPane.showMessageDialog( this,\r
"Could not read from " + url + "\n"\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
catch ( final Exception e ) {\r
JOptionPane.showMessageDialog( this,\r
static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
} // MainFrameApplication.\r
import org.forester.analysis.AncestralTaxonomyInference;
import org.forester.analysis.AncestralTaxonomyInferenceException;
+import org.forester.archaeopteryx.MainFrame;
import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.archaeopteryx.TreePanel;
import org.forester.phylogeny.Phylogeny;
public class AncestralTaxonomyInferrer extends RunnableProcess {
private final Phylogeny _phy;
- private final MainFrameApplication _mf;
+ private final MainFrame _mf;
private final TreePanel _treepanel;
- public AncestralTaxonomyInferrer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
+ public AncestralTaxonomyInferrer( final MainFrame mf, final TreePanel treepanel, final Phylogeny phy ) {
_phy = phy;
_mf = mf;
_treepanel = treepanel;
git://source.jalview.org / jalview.git / commitdiff