import javax.swing.Box;\r
import javax.swing.JApplet;\r
import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFileChooser;\r
import javax.swing.JFrame;\r
import javax.swing.JLabel;\r
import javax.swing.JMenu;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.ProcessPool;\r
import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
+import org.forester.archaeopteryx.webservices.WebservicesManager;\r
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
import org.forester.phylogeny.Phylogeny;\r
import org.forester.phylogeny.PhylogenyMethods;\r
import org.forester.phylogeny.PhylogenyNode;\r
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.NodeDataField;\r
import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
import org.forester.sdi.SDIException;\r
import org.forester.util.ForesterConstants;\r
import org.forester.util.ForesterUtil;\r
+import org.forester.util.WindowsUtils;\r
\r
public abstract class MainFrame extends JFrame implements ActionListener {\r
\r
static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
private static final long serialVersionUID = 3655000897845508358L;\r
final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
static final String OPTIONS_HEADER = "Options";\r
static final String SEARCH_SUBHEADER = "Search:";\r
static final String DISPLAY_SUBHEADER = "Display:";\r
static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
+ static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\r
static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
+ static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
static final String BG_GRAD_LABEL = "Background Color Gradient";\r
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
static final String SHOW_OVERVIEW_LABEL = "Overview";\r
static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
JMenuItem _close_item;\r
JMenuItem _exit_item;\r
JMenuItem _new_item;\r
+ JMenuItem _print_item;\r
+ JMenuItem _write_to_pdf_item;\r
+ JMenuItem _write_to_jpg_item;\r
+ JMenuItem _write_to_gif_item;\r
+ JMenuItem _write_to_tif_item;\r
+ JMenuItem _write_to_png_item;\r
+ JMenuItem _write_to_bmp_item;\r
// tools menu:\r
JMenuItem _midpoint_root_item;\r
JMenuItem _taxcolor_item;\r
JMenuItem _confcolor_item;\r
JMenuItem _color_rank_jmi;\r
JMenuItem _collapse_species_specific_subtrees;\r
- JMenuItem _collapse_below_threshold; //TODO implememt me\r
JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
JMenuItem _obtain_seq_information_jmi;\r
JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
JCheckBoxMenuItem _show_overview_cbmi;\r
JCheckBoxMenuItem _show_domain_labels;\r
JCheckBoxMenuItem _show_annotation_ref_source;\r
JMenuItem _choose_minimal_confidence_mi;\r
JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
JMenuItem _cycle_node_shape_mi;\r
JMenuItem _cycle_node_fill_mi;\r
JMenuItem _choose_node_size_mi;\r
+ JMenuItem _cycle_data_return;\r
JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
JCheckBoxMenuItem _search_case_senstive_cbmi;\r
JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
JCheckBoxMenuItem _inverse_search_result_cbmi;\r
+ JCheckBoxMenuItem _search_with_regex_cbmi;\r
// type menu:\r
JMenu _type_menu;\r
JCheckBoxMenuItem _rectangular_type_cbmi;\r
JMenuItem _phyloxml_website_item;\r
JMenuItem _phyloxml_ref_item;\r
JMenuItem _aptx_ref_item;\r
+ //\r
+ JFileChooser _writetopdf_filechooser;\r
+ File _current_dir;\r
+ \r
// process menu:\r
JMenu _process_menu;\r
// Handy pointers to child components:\r
MainPanel _mainpanel;\r
Container _contentpane;\r
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
Configuration _configuration;\r
Options _options;\r
private Phylogeny _species_tree;\r
\r
MainFrame() {\r
_process_pool = ProcessPool.createInstance();\r
+ _writetopdf_filechooser = new JFileChooser();\r
}\r
\r
/**\r
switchColors();\r
}\r
else if ( o == _display_basic_information_item ) {\r
- displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+ }\r
}\r
else if ( o == _view_as_NH_item ) {\r
viewAsNH();\r
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
}\r
else if ( o == _cycle_node_fill_mi ) {\r
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeFill( getOptions() );\r
}\r
else if ( o == _cycle_node_shape_mi ) {\r
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeShape( getOptions() );\r
+ }\r
+ else if ( o == _cycle_data_return ) {\r
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
}\r
else if ( o == _screen_antialias_cbmi ) {\r
updateOptions( getOptions() );\r
else if ( o == _show_default_node_shapes_external_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
else if ( o == _non_lined_up_cladograms_rbmi ) {\r
updateOptions( getOptions() );\r
showWhole();\r
getMainPanel().getControlPanel().search1();\r
}\r
else if ( o == _search_whole_words_only_cbmi ) {\r
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
+ _search_with_regex_cbmi.setSelected( false );\r
+ }\r
updateOptions( getOptions() );\r
getMainPanel().getControlPanel().search0();\r
getMainPanel().getControlPanel().search1();\r
getMainPanel().getControlPanel().search0();\r
getMainPanel().getControlPanel().search1();\r
}\r
+ else if ( o == _search_with_regex_cbmi ) {\r
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_whole_words_only_cbmi.setSelected( false );\r
+ }\r
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_case_senstive_cbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
else if ( o == _show_scale_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
}\r
}\r
+ else if ( o == _write_to_pdf_item ) {\r
+ writeToPdf( _mainpanel.getCurrentPhylogeny() );\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
_contentpane.repaint();\r
}\r
\r
+ \r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ } \r
+ \r
+ void writeToPdf( final Phylogeny t ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + ".pdf";\r
+ _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetopdf_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ printPhylogenyToPdf( file.toString() );\r
+ }\r
+ }\r
+\r
+ \r
+ void printPhylogenyToPdf( final String file_name ) {\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel()\r
+ .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( getOptions().isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ getCurrentTreePanel(),\r
+ getCurrentTreePanel().getWidth(),\r
+ getCurrentTreePanel().getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+ .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
+ }\r
+ \r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ \r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
+ }\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
+ }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ }\r
+ }\r
+ return _current_dir;\r
+ }\r
+ \r
private void deleteSelectedNodes( final boolean delete ) {\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\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
* has been selected by the user by clicking the "Return ..."\r
* menu item. This method is expected to be called from Javascript or\r
* something like it.\r
- * \r
+ *\r
* @return current external node data as String\r
*/\r
public String getCurrentExternalNodesDataBuffer() {\r
}\r
}\r
\r
+// void buildFileMenu() {\r
+// _file_jmenu = createMenu( "File", getConfiguration() );\r
+// _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+// customizeJMenuItem( _exit_item );\r
+// _jmenubar.add( _file_jmenu );\r
+// }\r
+ \r
void buildFileMenu() {\r
- _file_jmenu = createMenu( "File", getConfiguration() );\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ \r
+ // _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ // _save_all_item.setEnabled( false );\r
+ // _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+// if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+// _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+// }\r
+// _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+// _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+// if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+// _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+// }\r
+// if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+// _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+// }\r
+ // _file_jmenu.addSeparator();\r
+ // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+\r
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ \r
+ customizeJMenuItem( _save_item );\r
+\r
+// customizeJMenuItem( _close_item );\r
+ //customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+// customizeJMenuItem( _write_to_png_item );\r
+// customizeJMenuItem( _write_to_jpg_item );\r
+// customizeJMenuItem( _write_to_gif_item );\r
+// customizeJMenuItem( _write_to_tif_item );\r
+// customizeJMenuItem( _write_to_bmp_item );\r
+// customizeJMenuItem( _print_item );\r
customizeJMenuItem( _exit_item );\r
_jmenubar.add( _file_jmenu );\r
}\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
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
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
}\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
"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
return label;\r
}\r
\r
- static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeFill( final Options op ) {\r
switch ( op.getDefaultNodeFill() ) {\r
case GRADIENT:\r
op.setDefaultNodeFill( NodeFill.SOLID );\r
}\r
}\r
\r
- static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeShape( final Options op ) {\r
switch ( op.getDefaultNodeShape() ) {\r
case CIRCLE:\r
op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
}\r
}\r
\r
+ private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+ ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+ }\r
+ else {\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ break; \r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ }\r
+\r
static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
switch ( op.getOvPlacement() ) {\r
case LOWER_LEFT:\r
}\r
}\r
\r
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+ mi.setText( "Cycle Node Return Data... (current: "\r
+ + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
+ }\r
+ }\r
+\r
static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\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
git://source.jalview.org / jalview.git / blobdiff