public TreeAccuracyInformation checkAccuracy() throws Exception {
Phylogeny p = treeConstructor.getPhylogeny();
if (p == null) throw new Exception("Run process() method before this one.");
CheckTreeAccuracy acc = new CheckTreeAccuracy();
acc.process(p, treeConstructor.getDistanceMatrix());
TreeAccuracyInformation tai = new TreeAccuracyInformation();
tai.setAverageMatrixDistance(acc.getAverageMatrixDistance());
tai.setAverageTreeDistance(acc.getAverageTreeDistance());
tai.setAverageErrorRate(acc.getAverageTreeErrorDistance());
return tai;
}
/**
* Budowanie drzewa metodą Neighbour Joining. http://en.wikipedia.org/wiki/Neighbour_joining
*
* @return drzewo w formie Newick (zanawiasowane)
*/
public String NeighbourJoining() {
alignSequences();
treeConstructor =
new TreeConstructor<ProteinSequence, AminoAcidCompound>(
multipleSequenceAlignment,
TreeType.NJ,
TreeConstructionAlgorithm.PID,
new ProgessListenerStub());
String newick = null;
try {
treeConstructor.process();
newick = treeConstructor.getNewickString(true, true);
} catch (Exception ex) {
Logger.getLogger(TreeBuilder.class.getName()).log(Level.SEVERE, null, ex);
}
return newick;
}