X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=8689bd4c8be27ef851b8e7c70681965c5f081058;hb=0bcaf88108ac7d33e5a76df7fa49bf22d01c6798;hp=a8c58ee4c3a38052244e78299c753ebb58f82c6e;hpb=8a0a03d1fe15e36142994518585a185fb0ea6543;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index a8c58ee..8689bd4 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,7 +34,6 @@ import java.io.IOException; import java.util.LinkedList; import java.util.List; import java.util.Locale; -import java.util.Map; import java.util.NoSuchElementException; import java.util.Set; @@ -58,12 +57,17 @@ import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.tools.InferenceManager; import org.forester.archaeopteryx.tools.ProcessPool; import org.forester.archaeopteryx.tools.ProcessRunning; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.NodeVisualization.NodeFill; import org.forester.phylogeny.data.NodeVisualization.NodeShape; +import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; @@ -100,7 +104,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; static final String BG_GRAD_LABEL = "Background Color Gradient"; - static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes"; static final String SHOW_OVERVIEW_LABEL = "Show Overview"; static final String FONT_SIZE_MENU_LABEL = "Font Size"; static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; @@ -122,6 +127,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenu _font_size_menu; JMenu _help_jmenu; JMenuItem[] _load_phylogeny_from_webservice_menu_items; + // Analysis menu + JMenu _analysis_menu; + JMenuItem _load_species_tree_item; + JMenuItem _gsdi_item; + JMenuItem _gsdir_item; + JMenuItem _lineage_inference; + JMenuItem _function_analysis; // file menu: JMenuItem _open_item; JMenuItem _open_url_item; @@ -169,7 +181,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _color_labels_same_as_parent_branch; JMenuItem _overview_placment_mi; JMenuItem _choose_minimal_confidence_mi; - JCheckBoxMenuItem _show_default_node_shapes_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; @@ -185,7 +198,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _choose_pdf_width_mi; // _ parsing JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; - JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi; + JRadioButtonMenuItem _extract_taxonomy_no_rbmi; + JRadioButtonMenuItem _extract_taxonomy_yes_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi; JCheckBoxMenuItem _replace_underscores_cbmi; JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; @@ -205,7 +220,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _circular_type_cbmi; // view as text menu: JMenuItem _view_as_NH_item; - JMenuItem _view_as_NHX_item; JMenuItem _view_as_XML_item; JMenuItem _view_as_nexus_item; JMenuItem _display_basic_information_item; @@ -225,6 +239,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; + Phylogeny _species_tree; InferenceManager _inference_manager; final ProcessPool _process_pool; private String _previous_node_annotation_ref; @@ -253,6 +268,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _exit_item ) { close(); } + else if ( o == _gsdi_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDI(); + } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } else if ( o == _taxcolor_item ) { taxColor(); } @@ -294,9 +321,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _view_as_NH_item ) { viewAsNH(); } - else if ( o == _view_as_NHX_item ) { - viewAsNHX(); - } else if ( o == _view_as_XML_item ) { viewAsXML(); } @@ -367,7 +391,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _color_labels_same_as_parent_branch ) { updateOptions( getOptions() ); } - else if ( o == _show_default_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_internal_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { @@ -436,7 +463,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -486,6 +513,26 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _configuration; } + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + public InferenceManager getInferenceManager() { return _inference_manager; } @@ -607,11 +654,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) ); - _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) ); _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); - customizeJMenuItem( _view_as_NHX_item ); customizeJMenuItem( _view_as_XML_item ); customizeJMenuItem( _view_as_nexus_item ); _jmenubar.add( _view_jmenu ); @@ -737,6 +782,147 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); } + void executeGSDI() { + if ( !isOKforSDI( false, true ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not rooted.", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDI gsdi = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdi = new GSDI( gene_tree, species_tree, false, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + gene_tree.setRerootable( false ); + gene_tree.clearHashIdToNodeMap(); + gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + void executeGSDIR() { + if ( !isOKforSDI( false, false ) ) { + return; + } + final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); + if ( ( p > 0 ) + && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDIR gsdir = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDIR", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); + result_gene_tree.setRerootable( false ); + result_gene_tree.clearHashIdToNodeMap(); + result_gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { JOptionPane.showMessageDialog( this, @@ -773,7 +959,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _jmenubar; } - void help( final Map weblinks ) { + void help() { final StringBuilder sb = new StringBuilder(); sb.append( "Display options\n" ); sb.append( "-------------------\n" ); @@ -811,14 +997,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" ); sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" ); sb.append( "the '-Xmx' Java command line option. For example:\n" ); - sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" ); - if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) { - sb.append( "Active web links\n" ); - sb.append( "--------------------\n" ); - for( final String key : weblinks.keySet() ) { - sb.append( " " + weblinks.get( key ).toString() + "\n" ); - } - } + sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" ); // + "General remarks\n" // + "---------------\n" // + @@ -859,14 +1038,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { // + " incorrect and need to be inferred again\n" // + // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n" - sb.append( "\n" ); sb.append( "phyloXML\n" ); sb.append( "-------------------\n" ); sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" ); sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" ); sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); sb.append( "\n" ); - sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" ); + sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" ); sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" ); TextFrame.instantiate( sb.toString(), "Help", _textframes ); } @@ -901,6 +1079,36 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Species tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else { + return true; + } + } + boolean isSubtreeDisplayed() { if ( getCurrentTreePanel() != null ) { if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { @@ -1044,8 +1252,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) - && _show_default_node_shapes_cbmi.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { @@ -1096,8 +1306,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); - options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null ) - && _extract_pfam_style_tax_codes_cbmi.isSelected() ); + if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) { + options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE ); + } + else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) { + options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { + options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO ); + } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) && _replace_underscores_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) @@ -1168,16 +1385,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void viewAsNHX() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "NHX"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; - } - showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title ); - } - } - void viewAsXML() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; @@ -1190,7 +1397,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { private void annotateSequences() { if ( getCurrentTreePanel() != null ) { - final Set nodes = getCurrentTreePanel().getFoundNodes(); + final Set nodes = getCurrentTreePanel().getFoundNodes(); if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane .showMessageDialog( this, @@ -1239,7 +1446,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { desc = desc.replaceAll( "\\s+", " " ); } if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { - for( final Integer id : nodes ) { + for( final Long id : nodes ) { final PhylogenyNode n = phy.getNode( id ); ForesterUtil.ensurePresenceOfSequence( n ); final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() @@ -1256,14 +1463,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - private String getPreviousNodeAnnotationReference() { - return _previous_node_annotation_ref; - } - - private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { - _previous_node_annotation_ref = previous_node_annotation_ref; - } - private void chooseFont() { final FontChooser fc = new FontChooser(); fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); @@ -1328,18 +1527,26 @@ public abstract class MainFrame extends JFrame implements ActionListener { repaint(); } + private String getPreviousNodeAnnotationReference() { + return _previous_node_annotation_ref; + } + private void removeBranchColors() { if ( getMainPanel().getCurrentPhylogeny() != null ) { AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); } } + private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { + _previous_node_annotation_ref = previous_node_annotation_ref; + } + /** * Display the about box. */ static void about() { final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" ); + about.append( "Copyright (C) 2013 Christian M. Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); about.append( "Last modified: " + Constants.PRG_DATE + "\n" );