final List<PhylogenyNode> qnode_ext_nodes = qnode_pp.getAllExternalDescendants();
final int lec_ext_nodes = qnode_ext_nodes.size() - 1;
final int p_ext_nodes = p.getNumberOfExternalNodes() - 1;
- final List<String> qnode_ext_nodes_names = new ArrayList<>();
+ final List<String> qnode_ext_nodes_names = new ArrayList<String>();
for( final PhylogenyNode qnode_ext_node : qnode_ext_nodes ) {
String name = qnode_ext_node.getName();
if ( ForesterUtil.isEmptyTrimmed( name ) ) {
}
res.setLeastEncompassingCladeSize( lec_ext_nodes );
res.setTreeSize( p_ext_nodes );
-
final String conf = obtainConfidence( qnode_pp );
if ( conf != null ) {
- res.setGreatestCommonCladeSubtreeConfidence(conf);
+ res.setGreatestCommonCladeSubtreeConfidence( conf );
}
-
final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator );
res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
if ( greatest_common_prefix_up[ 1 ] != null ) {
return res;
}
-
-
private final static String[] analyzeSiblings( final PhylogenyNode child,
final PhylogenyNode parent,
final String separator ) {
final int child_index = child.getChildNodeIndex();
- final List<String> ext_nodes_names = new ArrayList<>();
+ final List<String> ext_nodes_names = new ArrayList<String>();
final List<PhylogenyNode> descs = parent.getDescendants();
String conf = null;
for( int i = 0; i < descs.size(); ++i ) {
final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator );
return new String[] { greatest_common_prefix, conf };
}
-
+
private final static String obtainConfidence( final PhylogenyNode n ) {
- if ( n.getBranchData().getConfidences() != null && n.getBranchData().getConfidences().size() > 0 ) {
+ if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) {
final List<Confidence> confidences = n.getBranchData().getConfidences();
boolean not_first = false;
Collections.sort( confidences );