X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=0866f1c9cbf20971536c98044704fd47acbc68ff;hb=30ea6e22e29814b611cf523d0b39b9e0197e63dc;hp=72f2e27bcde4a7b3e5cd0a008a8d2ad0dd6aa97e;hpb=a5c10503459aaada602af51a0169b568ada036b4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 72f2e27..0866f1c 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; @@ -30,11 +30,11 @@ import java.awt.Container; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.io.File; 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; @@ -60,11 +60,16 @@ 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.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; 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.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.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; @@ -92,8 +97,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; - static final String DISPLAY_SCALE_LABEL = "Display Scale"; + static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values"; + static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; + static final String DISPLAY_SCALE_LABEL = "Scale"; static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; static final String LABEL_DIRECTION_LABEL = "Radial Labels"; @@ -101,20 +107,23 @@ 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 SHOW_OVERVIEW_LABEL = "Show Overview"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes"; + static final String SHOW_OVERVIEW_LABEL = "Overview"; static final String FONT_SIZE_MENU_LABEL = "Font Size"; static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; - static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; + static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; + static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; - static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations"; + static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations"; static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; + static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -123,9 +132,14 @@ 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; // file menu: JMenuItem _open_item; - JMenuItem _open_url_item; JMenuItem _save_item; JMenuItem _save_all_item; JMenuItem _close_item; @@ -163,18 +177,20 @@ public abstract class MainFrame extends JFrame implements ActionListener { JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _show_branch_length_values_cbmi; + JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; + JCheckBoxMenuItem _show_annotation_ref_source; JCheckBoxMenuItem _abbreviate_scientific_names; 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; - JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; JCheckBoxMenuItem _show_confidence_stddev_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; @@ -187,9 +203,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { // _ parsing JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; JRadioButtonMenuItem _extract_taxonomy_no_rbmi; - JRadioButtonMenuItem _extract_taxonomy_yes_rbmi; - JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi; + JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; JCheckBoxMenuItem _replace_underscores_cbmi; + JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi; JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; // _ search @@ -208,7 +226,6 @@ 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; @@ -228,6 +245,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; + private Phylogeny _species_tree; InferenceManager _inference_manager; final ProcessPool _process_pool; private String _previous_node_annotation_ref; @@ -250,12 +268,21 @@ public abstract class MainFrame extends JFrame implements ActionListener { applet = getCurrentTreePanel().obtainApplet(); } } - if ( o == _open_url_item ) { - readPhylogeniesFromURL(); - } - else if ( o == _exit_item ) { + 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(); } @@ -292,14 +319,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { switchColors(); } else if ( o == _display_basic_information_item ) { - displayBasicInformation(); + displayBasicInformation( getCurrentTreePanel().getTreeFile() ); } else if ( o == _view_as_NH_item ) { viewAsNH(); } - else if ( o == _view_as_NHX_item ) { - viewAsNHX(); - } else if ( o == _view_as_XML_item ) { viewAsXML(); } @@ -364,16 +388,19 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_domain_labels ) { updateOptions( getOptions() ); } + else if ( o == _show_annotation_ref_source ) { + updateOptions( getOptions() ); + } else if ( o == _abbreviate_scientific_names ) { updateOptions( getOptions() ); } 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 == _taxonomy_colorize_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } else if ( o == _non_lined_up_cladograms_rbmi ) { @@ -390,15 +417,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { } 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() ); @@ -406,6 +436,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_branch_length_values_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } else if ( o == _show_confidence_stddev_cbmi ) { updateOptions( getOptions() ); } @@ -439,7 +472,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -557,10 +590,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { void buildFileMenu() { _file_jmenu = createMenu( "File", getConfiguration() ); - _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) ); - _file_jmenu.addSeparator(); _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); - customizeJMenuItem( _open_url_item ); customizeJMenuItem( _exit_item ); _jmenubar.add( _file_jmenu ); } @@ -626,15 +656,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { void buildViewMenu() { _view_jmenu = createMenu( "View", getConfiguration() ); - _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( 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 ); @@ -727,13 +755,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void displayBasicInformation() { + void displayBasicInformation( final File treefile ) { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title ); + showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title ); } } @@ -760,6 +788,148 @@ 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 = getSpeciesTree().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 = getSpeciesTree().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 ); + } + } + boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { JOptionPane.showMessageDialog( this, @@ -796,7 +966,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _jmenubar; } - void help( final Map weblinks ) { + final Phylogeny getSpeciesTree() { + return _species_tree; + } + + void help() { final StringBuilder sb = new StringBuilder(); sb.append( "Display options\n" ); sb.append( "-------------------\n" ); @@ -834,14 +1008,7 @@ 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" // + @@ -882,14 +1049,13 @@ 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 ); } @@ -924,6 +1090,36 @@ 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 ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !getSpeciesTree().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() ) { @@ -944,8 +1140,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - abstract void readPhylogeniesFromURL(); - void readPhylogeniesFromWebservice( final int i ) { final UrlTreeReader reader = new UrlTreeReader( this, i ); new Thread( reader ).start(); @@ -1004,6 +1198,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + final void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + void setTypeMenuToAllUnselected() { _convex_type_cbmi.setSelected( false ); _curved_type_cbmi.setSelected( false ); @@ -1063,14 +1261,16 @@ public abstract class MainFrame extends JFrame 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.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_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() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1099,6 +1299,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) && ( _print_using_actual_size_cbmi.isSelected() ) ); options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) @@ -1119,17 +1322,22 @@ 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() ); - if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.YES ); + if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } - else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO ); + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) && _replace_underscores_cbmi.isSelected() ); + options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) + && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) @@ -1179,7 +1387,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), title ); @@ -1190,7 +1398,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny() .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), @@ -1198,21 +1406,11 @@ 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"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } @@ -1220,7 +1418,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { private void annotateSequences() { if ( getCurrentTreePanel() != null ) { - final Set nodes = getCurrentTreePanel().getFoundNodes(); + final Set nodes = getCurrentTreePanel().getFoundNodes0(); if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane .showMessageDialog( this, @@ -1269,7 +1467,7 @@ 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() @@ -1369,7 +1567,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { */ 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" );