+ public final Phylogeny calcTree() {
+ final Phylogeny phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, false, "" );
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ final boolean x = PhylogenyMethods.extractFastaInformation( phy );
+ if ( !x ) {
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ try {
+ ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ // Ignore.
+ }
+ }
+ }
+ }
+ return phy;
+ }
+
+ public final void decorateTree( final Phylogeny phy, final List<String> to_remove_ids ) {
+ for( int i = 0; i < to_remove_ids.size(); ++i ) {
+ final String id = to_remove_ids.get( i );
+ final PhylogenyNode n = phy.getNode( id );
+ n.setName( n.getName() + " [" + ( i + 1 ) + "]" );
+ final NodeVisualData vis = new NodeVisualData();
+ vis.setFillType( NodeFill.SOLID );
+ vis.setShape( NodeShape.RECTANGLE );
+ vis.setSize( 6 );
+ vis.setNodeColor( new Color( i > 255 ? 0 : 255 - i, 0, 0 ) );
+ n.getNodeData().setNodeVisualData( vis );
+ }
+ }
+
+ public final void decorateTree2( final Phylogeny phy, final List<MsaProperties> msa_props ) {
+ final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics();
+ for( int i = 0; i < msa_props.size(); ++i ) {
+ final MsaProperties msa_prop = msa_props.get( i );
+ final String id = msa_prop.getRemovedSeq();
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ length_stats.addValue( msa_prop.getLength() );
+ }
+ }
+ final double mean = length_stats.arithmeticMean();
+ final double min = length_stats.getMin();
+ final double max = length_stats.getMax();
+ final Color min_color = new Color( 0, 255, 0 );
+ final Color max_color = new Color( 255, 0, 0 );
+ final Color mean_color = new Color( 255, 255, 0 );
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final NodeVisualData vis = new NodeVisualData();
+ vis.setFillType( NodeFill.SOLID );
+ vis.setShape( NodeShape.RECTANGLE );
+ vis.setSize( 6 );
+ vis.setNodeColor( min_color );
+ it.next().getNodeData().setNodeVisualData( vis );
+ }
+ for( int i = 0; i < msa_props.size(); ++i ) {
+ final MsaProperties msa_prop = msa_props.get( i );
+ final String id = msa_prop.getRemovedSeq();
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ final PhylogenyNode n = phy.getNode( id );
+ n.setName( n.getName() + " [" + i + "]" );
+ n.getNodeData()
+ .getNodeVisualData()
+ .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
+ min,
+ max,
+ mean,
+ min_color,
+ max_color,
+ mean_color ) );
+ }
+ }
+ }
+
+ public final void displayTree( final Phylogeny phy ) {
+ final Configuration config = new Configuration();
+ config.setDisplayAsPhylogram( true );
+ config.setUseStyle( true );
+ config.setDisplayTaxonomyCode( false );
+ config.setDisplayTaxonomyCommonNames( false );
+ config.setDisplayTaxonomyScientificNames( false );
+ config.setDisplaySequenceNames( false );
+ config.setDisplaySequenceSymbols( false );
+ config.setDisplayGeneNames( false );
+ config.setShowScale( true );
+ config.setAddTaxonomyImagesCB( false );
+ config.setBaseFontSize( 9 );
+ config.setBaseFontFamilyName( "Arial" );
+ Archaeopteryx.createApplication( phy, config, _infile_name );
+ }
+