X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=f414cd7f2f25a853645bd83b19a67638be701d7b;hb=733f051a048f64b6850314a08880f1f77a633db8;hp=8a6730a92d99456a9e8ce0755394a74db5a83cd0;hpb=3d6a64e0371ffedf725bf8467211ed860f298550;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 8a6730a..f414cd7 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -98,10 +98,6 @@ import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.sdi.GSDI; -import org.forester.sdi.GSDIR; -import org.forester.sdi.SDIException; -import org.forester.sdi.SDIR; import org.forester.sequence.Sequence; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.BasicTable; @@ -137,15 +133,6 @@ public final class MainFrameApplication extends MainFrame { private final JFileChooser _save_filechooser; private final JFileChooser _writetopdf_filechooser; private final JFileChooser _writetographics_filechooser; - // Analysis menu - private JMenu _analysis_menu; - private JMenuItem _load_species_tree_item; - private JMenuItem _gsdi_item; - private JMenuItem _gsdir_item; - private JMenuItem _root_min_dups_item; - private JMenuItem _root_min_cost_l_item; - private JMenuItem _lineage_inference; - private JMenuItem _function_analysis; // Application-only print menu items private JMenuItem _print_item; private JMenuItem _write_to_pdf_item; @@ -154,7 +141,6 @@ public final class MainFrameApplication extends MainFrame { private JMenuItem _write_to_tif_item; private JMenuItem _write_to_png_item; private JMenuItem _write_to_bmp_item; - private Phylogeny _species_tree; private File _current_dir; private ButtonGroup _radio_group_1; private ButtonGroup _radio_group_2; @@ -279,7 +265,6 @@ public final class MainFrameApplication extends MainFrame { setInferenceManager( InferenceManager.createInstance( _configuration ) ); setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); // _textframe = null; #~~~~ - _species_tree = null; // set title setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" ); _mainpanel = new MainPanel( _configuration, this ); @@ -520,30 +505,6 @@ public final class MainFrameApplication extends MainFrame { else if ( o == _extract_tax_code_from_node_names_jmi ) { extractTaxDataFromNodeNames(); } - else if ( o == _gsdi_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeGSDI(); - } - else if ( o == _gsdir_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeGSDIR(); - } - else if ( o == _root_min_dups_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeSDIR( false ); - } - else if ( o == _root_min_cost_l_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeSDIR( true ); - } else if ( o == _graphics_export_visible_only_cbmi ) { updateOptions( getOptions() ); } @@ -805,16 +766,10 @@ public final class MainFrameApplication extends MainFrame { 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 (re-rooting)" ) ); - _analysis_menu.addSeparator(); - _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) ); - _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) ); - _analysis_menu.addSeparator(); + _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) ); customizeJMenuItem( _gsdi_item ); customizeJMenuItem( _gsdir_item ); - customizeJMenuItem( _root_min_dups_item ); - customizeJMenuItem( _root_min_cost_l_item ); customizeJMenuItem( _load_species_tree_item ); _analysis_menu.addSeparator(); _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); @@ -1175,98 +1130,6 @@ public final class MainFrameApplication extends MainFrame { new Thread( a ).start(); } - void executeGSDI() { - if ( !isOKforSDI( false, true ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not rooted.", - "Cannot execute GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDI gsdi = null; - final Phylogeny species_tree = _species_tree.copy(); - try { - gsdi = new GSDI( gene_tree, species_tree, false, true, true ); - } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; - } - gene_tree.setRerootable( false ); - _mainpanel.getCurrentTreePanel().setTree( gene_tree ); - _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap(); - _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true ); - _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - 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 ); - JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n" - + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: " - + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE ); - } - - void executeGSDIR() { - if ( !isOKforSDI( false, true ) ) { - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - GSDIR gsdir = null; - final Phylogeny species_tree = _species_tree.copy(); - try { - gsdir = new GSDIR( gene_tree, species_tree, true, true ); - } - catch ( final SDIException e ) { - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Error during GSDIR", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - AptxUtil.unexpectedException( e ); - return; - } - final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); - result_gene_tree.setRerootable( false ); - result_gene_tree.clearHashIdToNodeMap(); - result_gene_tree.recalculateNumberOfExternalDescendants( true ); - _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); - 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 ); - JOptionPane.showMessageDialog( this, - "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: " - + gsdir.getSpeciationsSum(), - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - void executeLineageInference() { if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { return; @@ -1285,37 +1148,6 @@ public final class MainFrameApplication extends MainFrame { new Thread( inferrer ).start(); } - void executeSDIR( final boolean minimize_cost ) { - if ( !isOKforSDI( true, true ) ) { - return; - } - Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - final SDIR sdiunrooted = new SDIR(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - try { - gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost - !minimize_cost, // minimize sum of dups - true, // minimize height - true, // return tree(s) - 1 )[ 0 ]; // # of trees to return - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE ); - return; - } - final int duplications = sdiunrooted.getMinimalDuplications(); - gene_tree.setRerootable( false ); - _mainpanel.getCurrentTreePanel().setTree( gene_tree ); - getControlPanel().setShowEvents( true ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - JOptionPane.showMessageDialog( this, - "Number of duplications: " + duplications, - "SDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - void exit() { removeAllTextFrames(); _mainpanel.terminate(); @@ -1325,36 +1157,6 @@ public final class MainFrameApplication extends MainFrame { System.exit( 0 ); } - 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 SDI", - 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 SDI", - 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 SDI", - JOptionPane.ERROR_MESSAGE ); - return false; - } - else { - return true; - } - } - @Override void readPhylogeniesFromURL() { URL url = null; @@ -1489,6 +1291,118 @@ public final class MainFrameApplication extends MainFrame { _contentpane.repaint(); } + private void addExpressionValuesFromFile() { + if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + JOptionPane.showMessageDialog( this, + "Need to load evolutionary tree first", + "Can Not Read Expression Values", + JOptionPane.WARNING_MESSAGE ); + return; + } + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _values_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _values_filechooser.showOpenDialog( _contentpane ); + final File file = _values_filechooser.getSelectedFile(); + if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + BasicTable t = null; + try { + t = BasicTableParser.parse( file, "\t" ); + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, "," ); + } + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, " " ); + } + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + e.getMessage(), + "Could Not Read Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( t.getNumberOfColumns() < 2 ) { + JOptionPane.showMessageDialog( this, + "Table contains " + t.getNumberOfColumns() + " column(s)", + "Problem with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( t.getNumberOfRows() < 1 ) { + JOptionPane.showMessageDialog( this, + "Table contains zero rows", + "Problem with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { + JOptionPane.showMessageDialog( this, + "Table contains " + t.getNumberOfRows() + " rows, but tree contains " + + phy.getNumberOfExternalNodes() + " external nodes", + "Warning", + JOptionPane.WARNING_MESSAGE ); + } + final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); + int not_found = 0; + for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + final String node_name = node.getName(); + if ( !ForesterUtil.isEmpty( node_name ) ) { + int row = -1; + try { + row = t.findRow( node_name ); + } + catch ( final IllegalArgumentException e ) { + JOptionPane + .showMessageDialog( this, + e.getMessage(), + "Error Mapping Node Identifiers to Expression Value Identifiers", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( row < 0 ) { + if ( node.isExternal() ) { + not_found++; + } + continue; + } + final List l = new ArrayList(); + for( int col = 1; col < t.getNumberOfColumns(); ++col ) { + double d = -100; + try { + d = Double.parseDouble( t.getValueAsString( col, row ) ); + } + catch ( final NumberFormatException e ) { + JOptionPane.showMessageDialog( this, + "Could not parse \"" + t.getValueAsString( col, row ) + + "\" into a decimal value", + "Issue with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + stats.addValue( d ); + l.add( d ); + } + if ( !l.isEmpty() ) { + if ( node.getNodeData().getProperties() != null ) { + node.getNodeData().getProperties() + .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); + } + node.getNodeData().setVector( l ); + } + } + } + if ( not_found > 0 ) { + JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found + + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); + } + getCurrentTreePanel().setStatisticsForExpressionValues( stats ); + } + } + private void addSequencesFromFile() { if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { JOptionPane.showMessageDialog( this, @@ -1645,127 +1559,6 @@ public final class MainFrameApplication extends MainFrame { } } - private void setArrowCursor() { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - } - - private void addExpressionValuesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Expression Values", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _values_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _values_filechooser.showOpenDialog( _contentpane ); - final File file = _values_filechooser.getSelectedFile(); - if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - BasicTable t = null; - try { - t = BasicTableParser.parse( file, "\t" ); - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, "," ); - } - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, " " ); - } - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - e.getMessage(), - "Could Not Read Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfColumns() < 2 ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfColumns() + " column(s)", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfRows() < 1 ) { - JOptionPane.showMessageDialog( this, - "Table contains zero rows", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfRows() + " rows, but tree contains " - + phy.getNumberOfExternalNodes() + " external nodes", - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - int not_found = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - final String node_name = node.getName(); - if ( !ForesterUtil.isEmpty( node_name ) ) { - int row = -1; - try { - row = t.findRow( node_name ); - } - catch ( final IllegalArgumentException e ) { - JOptionPane - .showMessageDialog( this, - e.getMessage(), - "Error Mapping Node Identifiers to Expression Value Identifiers", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( row < 0 ) { - if ( node.isExternal() ) { - not_found++; - } - continue; - } - final List l = new ArrayList(); - for( int col = 1; col < t.getNumberOfColumns(); ++col ) { - double d = -100; - try { - d = Double.parseDouble( t.getValueAsString( col, row ) ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + t.getValueAsString( col, row ) - + "\" into a decimal value", - "Issue with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - stats.addValue( d ); - l.add( d ); - } - if ( !l.isEmpty() ) { - if ( node.getNodeData().getProperties() != null ) { - node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); - } - node.getNodeData().setVector( l ); - } - } - } - if ( not_found > 0 ) { - JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found - + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); - } - getCurrentTreePanel().setStatisticsForExpressionValues( stats ); - } - } - private void choosePdfWidth() { final String s = ( String ) JOptionPane.showInputDialog( this, "Please enter the default line width for PDF export.\n" @@ -2507,7 +2300,7 @@ public final class MainFrameApplication extends MainFrame { } } if ( !exception && ( t != null ) ) { - _species_tree = t; + setSpeciesTree( t ); JOptionPane.showMessageDialog( this, "Species tree successfully loaded", "Species tree loaded", @@ -2518,6 +2311,15 @@ public final class MainFrameApplication extends MainFrame { } } + private void setArrowCursor() { + try { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + catch ( final Exception ex ) { + // Do nothing. + } + } + private void setCurrentDir( final File current_dir ) { _current_dir = current_dir; }