return stats;
}
- public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+ public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
final PhylogenyNode n = iter.next();
- if ( !n.isExternal() ) {
+ if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+ stats.addValue( n.getDistanceToParent() );
+ }
+ }
+ return stats;
+ }
+
+ public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+ final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
if ( n.getBranchData().isHasConfidences() ) {
- stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+ for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
+ final Confidence c = n.getBranchData().getConfidences().get( i );
+ if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
+ stats.add( i, new BasicDescriptiveStatistics() );
+ }
+ if ( !ForesterUtil.isEmpty( c.getType() ) ) {
+ if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
+ if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
+ throw new IllegalArgumentException( "support values in node [" + n.toString()
+ + "] appear inconsistently ordered" );
+ }
+ }
+ stats.get( i ).setDescription( c.getType() );
+ }
+ stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
+ }
}
}
}