Package edu.msu.cme.rdp.taxatree

Class UnifracTree

java.lang.Object

edu.msu.cme.rdp.taxatree.ConcretRoot<UnifracTaxon>

edu.msu.cme.rdp.taxatree.UnifracTree

public class UnifracTree
extends edu.msu.cme.rdp.taxatree.ConcretRoot<UnifracTaxon>

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	UnifracTree.UnifracResult

Field Summary

Fields inherited from class edu.msu.cme.rdp.taxatree.ConcretRoot

root, taxonMap

Constructor Summary

Constructors

Constructor	Description
UnifracTree()

Method Summary

Modifier and Type	Method	Description
void	addChild(UnifracTaxon child, int parentId)
void	addTaxon(int parent, int taxid, java.lang.String name, MCSample sample, float bl)
UnifracTree.UnifracResult	computeUnifrac()
UnifracTree.UnifracResult	computeUnifracSig(int permutations, boolean weighted)
UnifracTree.UnifracResult	computeWeightedUnifrac()
void	printLeaves()
void	refreshInnerTaxa()

Methods inherited from class edu.msu.cme.rdp.taxatree.ConcretRoot

biDirectionDepthFirst, getChild, getChildTaxon, getRootTaxid, getRootTaxonHodler, topDownVisit

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

UnifracTree

public UnifracTree()

Method Detail

computeUnifrac

public UnifracTree.UnifracResult computeUnifrac()

computeUnifracSig

public UnifracTree.UnifracResult computeUnifracSig(int permutations,
                                                   boolean weighted)

computeWeightedUnifrac

public UnifracTree.UnifracResult computeWeightedUnifrac()

printLeaves

public void printLeaves()

addChild

public void addChild(UnifracTaxon child,
                     int parentId)

Overrides:

addChild in class edu.msu.cme.rdp.taxatree.ConcretRoot<UnifracTaxon>

refreshInnerTaxa

public void refreshInnerTaxa()

addTaxon

public void addTaxon(int parent,
                     int taxid,
                     java.lang.String name,
                     MCSample sample,
                     float bl)