X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=a855d90980d607d2a398b9acc08edcd1ae92a970;hb=b819fa043cac2722618af63f0d4752ffa1a40890;hp=ba52ded3bb982c2748dd4b131d1203fc2a7b0182;hpb=e928c819cdb894764733f5d40441a8235a6c629a;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index ba52ded..a855d90 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; @@ -121,15 +126,29 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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(); } @@ -209,15 +228,15 @@ 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() ); @@ -280,7 +299,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -387,8 +406,8 @@ 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 ), @@ -443,7 +462,8 @@ 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() ); @@ -465,6 +485,41 @@ 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(); @@ -472,6 +527,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( !getConfiguration().isUseNativeUI() ) { _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); } + if ( getSpeciesTree() != null ) { + buildAnalysisMenu(); + } buildToolsMenu(); buildViewMenu(); buildFontSizeMenu(); @@ -509,6 +567,10 @@ 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(); @@ -530,8 +592,8 @@ 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 ); } @@ -551,6 +613,19 @@ 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" ) ); @@ -800,6 +875,148 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } + 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 ); + } + } + Configuration getConfiguration() { return _configuration; } @@ -816,7 +1033,7 @@ 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" ); @@ -849,20 +1066,6 @@ 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" ); @@ -909,6 +1112,50 @@ 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 ) { @@ -990,6 +1237,10 @@ 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 ); @@ -1183,7 +1434,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } private MainPanel getMainPanel() { - return _main_panel; + return _mainpanel; + } + + private Phylogeny getSpeciesTree() { + return _species_tree; } private boolean isScreenAntialias() { @@ -1197,7 +1452,11 @@ 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() {