X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=72bb43f4ad48a5bd4268df8b8915087e0b3f25fd;hb=d33a5a1d64863f9b0207e1da71151396cea74a38;hp=b1b6d9f6399db17b777377e875ed5352831bfe8d;hpb=ceb6173a0256d06fffbe04756755bb18052622fc;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index b1b6d9f..72bb43f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -13,7 +13,6 @@ import java.io.IOException; import java.net.URL; import java.util.LinkedList; import java.util.List; -import java.util.Map; import java.util.NoSuchElementException; import javax.swing.ButtonGroup; @@ -34,8 +33,14 @@ import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.data.SequenceRelation; +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; @@ -56,7 +61,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private final static String NAME = "ArchaeopteryxE"; private static final long serialVersionUID = -1220055577935759443L; private Configuration _configuration; - private MainPanelApplets _main_panel; + private MainPanelApplets _mainpanel; private JMenuBar _jmenubar; private JMenu _options_jmenu; private JMenu _font_size_menu; @@ -72,7 +77,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenu _view_jmenu; private JMenuItem _view_as_XML_item; private JMenuItem _view_as_NH_item; - private JMenuItem _view_as_NHX_item; private JMenuItem _view_as_nexus_item; private JMenuItem _display_basic_information_item; private JMenu _type_menu; @@ -92,12 +96,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _phyloxml_ref_item; private JMenuItem _aptx_ref_item; private JMenuItem _remove_branch_color_item; - private JMenuItem _infer_common_sn_names_item; private JCheckBoxMenuItem _show_domain_labels; + private JCheckBoxMenuItem _show_annotation_ref_source; private JCheckBoxMenuItem _color_labels_same_as_parent_branch; private JCheckBoxMenuItem _abbreviate_scientific_names; private JCheckBoxMenuItem _screen_antialias_cbmi; private JCheckBoxMenuItem _background_gradient_cbmi; + private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; private JRadioButtonMenuItem _uniform_cladograms_rbmi; private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; @@ -115,22 +120,37 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _collapse_species_specific_subtrees; private JMenuItem _overview_placment_mi; private ButtonGroup _radio_group_1; - private JCheckBoxMenuItem _show_default_node_shapes_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; private JMenuItem _cycle_node_shape_mi; private JMenuItem _cycle_node_fill_mi; private JMenuItem _choose_node_size_mi; private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; private JCheckBoxMenuItem _show_confidence_stddev_cbmi; private final LinkedList _textframes = new LinkedList(); + private JMenu _analysis_menu; + private JMenuItem _gsdi_item; + private JMenuItem _gsdir_item; + private Phylogeny _species_tree; - // private String _ext_node_data_buffer = ""; - // private int _ext_node_data_buffer_change_counter = 0; @Override public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); if ( o == _midpoint_root_item ) { getMainPanel().getCurrentTreePanel().midpointRoot(); } + else if ( o == _gsdi_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDI(); + } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } else if ( o == _taxcolor_item ) { getMainPanel().getCurrentTreePanel().taxColor(); } @@ -154,9 +174,6 @@ public class ArchaeopteryxE extends JApplet 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(); } @@ -213,27 +230,30 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } else if ( o == _uniform_cladograms_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } else if ( o == _ext_node_dependent_cladogram_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } else if ( o == _search_case_senstive_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _search_whole_words_only_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _inverse_search_result_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); @@ -247,6 +267,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _label_direction_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _abbreviate_scientific_names ) { + updateOptions( getOptions() ); + } else if ( o == _show_overview_cbmi ) { updateOptions( getOptions() ); if ( getCurrentTreePanel() != null ) { @@ -271,7 +294,10 @@ public class ArchaeopteryxE extends JApplet 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 ) { @@ -281,7 +307,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -315,6 +341,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); } } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } repaint(); } @@ -339,7 +368,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); } - public int getCurrentExternalNodesDataBufferCounter() { + public int getCurrentExternalNodesDataBufferChangeCounter() { return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); } @@ -388,8 +417,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { final ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos, - _main_panel.getWidth(), - _main_panel.getHeight(), + _mainpanel.getWidth(), + _mainpanel.getHeight(), getCurrentTreePanel(), getCurrentTreePanel().getControlPanel(), GraphicsExportType.valueOf( format ), @@ -423,17 +452,17 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { setupUI(); URL phys_url = null; Phylogeny[] phys = null; - final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); - AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string ); + final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str ); // Get URL to tree file - if ( phys_url_string != null ) { + if ( tree_url_str != null ) { try { - phys_url = new URL( phys_url_string ); + phys_url = new URL( tree_url_str ); } catch ( final Exception e ) { ForesterUtil.printErrorMessage( NAME, "error: " + e ); e.printStackTrace(); - JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string + JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); } } @@ -444,7 +473,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { getConfiguration().isValidatePhyloXmlAgainstSchema(), getConfiguration().isReplaceUnderscoresInNhParsing(), getConfiguration().isInternalNumberAreConfidenceForNhParsing(), - getConfiguration().getTaxonomyExtraction() ); + getConfiguration().getTaxonomyExtraction(), + getConfiguration().isMidpointReroot() ); } catch ( final Exception e ) { ForesterUtil.printErrorMessage( NAME, e.toString() ); @@ -466,6 +496,41 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else { AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url ); } + // + final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ); + if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { + AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" ); + Phylogeny[] species_trees = null; + try { + final URL species_tree_url = new URL( species_tree_url_str ); + species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, + configuration.isValidatePhyloXmlAgainstSchema(), + configuration.isReplaceUnderscoresInNhParsing(), + false, + TAXONOMY_EXTRACTION.NO, + false ); + } + 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 ); + } + if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { + AptxUtil.printAppletMessage( NAME, "successfully read species tree" ); + if ( species_trees[ 0 ].isEmpty() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is empty" ); + } + else if ( !species_trees[ 0 ].isRooted() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" ); + } + else { + setSpeciesTree( species_trees[ 0 ] ); + AptxUtil.printAppletMessage( NAME, "species tree OK" ); + } + } + } + // setVisible( false ); setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); _jmenubar = new JMenuBar(); @@ -473,6 +538,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( !getConfiguration().isUseNativeUI() ) { _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); } + if ( getSpeciesTree() != null ) { + buildAnalysisMenu(); + } buildToolsMenu(); buildViewMenu(); buildFontSizeMenu(); @@ -489,11 +557,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void componentResized( final ComponentEvent e ) { if ( getMainPanel().getCurrentTreePanel() != null ) { - getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel() - .getWidth(), - getMainPanel().getCurrentTreePanel() - .getHeight(), - false ); + getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() + .getCurrentTreePanel() + .getWidth(), + getMainPanel() + .getCurrentTreePanel() + .getHeight(), + getOptions() + .isAllowFontSizeChange() ); } } } ); @@ -507,6 +578,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } else { AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); + if ( getSpeciesTree() != null ) { + AptxUtil.printAppletMessage( NAME, + "Warning: gsdi (gene duplication inference) only available tabbed display" ); + } AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); } validate(); @@ -528,8 +603,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); if ( default_sequence != null ) { getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence ); - /* GUILHEM_END */ } + /* GUILHEM_END */ setVisible( true ); } @@ -549,6 +624,19 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { AptxUtil.printAppletMessage( NAME, "started" ); } + 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" ); + _jmenubar.add( _analysis_menu ); + } + void buildFontSizeMenu() { _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() ); _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) ); @@ -619,33 +707,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); _radio_group_1.add( _non_lined_up_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_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); + _options_jmenu + .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 ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _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( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); _options_jmenu .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 ) ); _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); - } + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + ///// _options_jmenu.addSeparator(); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -658,13 +753,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); - customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); @@ -699,9 +799,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); customizeJMenuItem( _midpoint_root_item ); _tools_menu.addSeparator(); - _tools_menu - .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) ); - customizeJMenuItem( _infer_common_sn_names_item ); _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); customizeJMenuItem( _collapse_species_specific_subtrees ); _jmenubar.add( _tools_menu ); @@ -733,15 +830,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildViewMenu() { _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); - _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu + .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( "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" ) ); + _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); + _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); + _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "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 ); @@ -792,9 +888,151 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title ); + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); + } + } + + 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, 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, 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 ); + PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + _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 ); } } @@ -814,7 +1052,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _options; } - void help( final Map weblinks ) { + void help() { final StringBuilder sb = new StringBuilder(); sb.append( "Display options\n" ); sb.append( "-------------------\n" ); @@ -847,20 +1085,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { sb.append( "------------------------\n" ); sb.append( "Order Subtrees -- order the tree by branch length\n" ); sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" ); - sb.append( "Memory problems (Java heap space error)\n" ); - sb.append( "---------------------------------------\n" ); - 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( "\n" ); sb.append( "phyloXML\n" ); sb.append( "-------------------\n" ); sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" ); @@ -907,6 +1131,50 @@ public class ArchaeopteryxE extends JApplet 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() ) { + 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 ); + return true; + } + } + return false; + } + void removeAllTextFrames() { for( final TextFrame tf : _textframes ) { if ( tf != null ) { @@ -988,6 +1256,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } + void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + void switchColors() { final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet(); final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); @@ -1023,12 +1295,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) && _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() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) && _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() ) ) { @@ -1087,6 +1363,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } } void updateTypeCheckboxes( final Options options, final Object o ) { @@ -1098,7 +1377,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() .getNhConversionSupportValueStyle() ), @@ -1110,7 +1389,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny() .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), @@ -1118,21 +1397,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - void viewAsNHX() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - String title = "NHX"; - if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; - } - showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title ); - } - } - void viewAsXML() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); } @@ -1189,7 +1458,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } private MainPanel getMainPanel() { - return _main_panel; + return _mainpanel; + } + + private Phylogeny getSpeciesTree() { + return _species_tree; } private boolean isScreenAntialias() { @@ -1203,7 +1476,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } private void setMainPanel( final MainPanelApplets main_panel ) { - _main_panel = main_panel; + _mainpanel = main_panel; + } + + private void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; } private void setupUI() {