- desc.append( "; " );
- desc.append( "maximum descendants: " );
- desc.append( PhylogenyMethods.calculateMaximumNumberOfDescendantsPerNode( phy ) );
- if ( !ForesterUtil.isEmpty( full_path ) && ( full_path.length() <= 50 ) ) {
- desc.append( "; " );
- desc.append( "path: " );
- desc.append( full_path );
+ desc.append( "\n" );
+ desc.append( "Depth: " );
+ desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
+ desc.append( "\n" );
+ desc.append( "Maximum distance to root: " );
+ desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
+ desc.append( "\n" );
+ desc.append( "Descendants per node statistics: " );
+ final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
+ desc.append( "\n" );
+ final DescriptiveStatistics cs = PhylogenyMethods.calculatConfidenceStatistics( phy );
+ if ( cs.getN() > 1 ) {
+ desc.append( "Support statistics: " );
+ desc.append( "\n" );
+ desc.append( " Branches with support: " + cs.getN() );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+ desc.append( "\n" );
+ if ( cs.getN() > 2 ) {
+ desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
+ desc.append( "\n" );
+ }
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( "\n" );
+ }
+ final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+ if ( taxs != null ) {
+ desc.append( "Distinct external taxonomies: " );
+ desc.append( taxs.size() );