+ 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 ) {