X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=c353213dab71757e1d41a35c6a290f7d3dd37a19;hb=9b8fed885e8d0687ac000a8d26ea4bb9bd45c6bf;hp=8079b121c0e8a5f69fe1328435d270084080adf5;hpb=761fedd91bd3c10855d8230111ecbc94bda59a24;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 8079b12..c353213 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -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; @@ -60,11 +59,16 @@ 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.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; @@ -116,6 +120,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SHOW_CONF_STDDEV_LABEL = "Show 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 = "Show Basic Tree Information"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -124,6 +129,13 @@ 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; @@ -229,6 +241,7 @@ 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; @@ -257,6 +270,18 @@ 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(); } @@ -440,7 +465,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -627,7 +652,7 @@ 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" ) ); @@ -759,6 +784,148 @@ 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, @@ -795,7 +962,11 @@ 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" ); @@ -833,14 +1004,7 @@ 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" // + @@ -881,7 +1045,6 @@ 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" ); @@ -923,6 +1086,36 @@ 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() ) { @@ -1003,6 +1196,10 @@ 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 ); @@ -1121,7 +1318,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { 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.AGRESSIVE ); + options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) { options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );