edu.msu.cme.rdp.classifier.comparison
Class TaxonTree

java.lang.Object
  edu.msu.cme.rdp.classifier.comparison.AbstractNode
      edu.msu.cme.rdp.classifier.comparison.TaxonTree

All Implemented Interfaces:

ComparisonBrowserNode, Taxon

public class TaxonTree
extends AbstractNode

Nested Class Summary

(package private) class	TaxonTree.DetailIterator An Iterator of the sequences assigned to the node
(package private) class	TaxonTree.SampleDetailIterator

Nested classes/interfaces inherited from class edu.msu.cme.rdp.classifier.comparison.AbstractNode

AbstractNode.LineageIterator, AbstractNode.TaxonIterator

Field Summary

private AbstractNode	firstChild
private Score	firstS1Score
private Score	firstS2Score
private Score	lastS1Score
private Score	lastS2Score
private java.lang.String	name
private java.lang.String	rank
private int	taxid

Constructor Summary

TaxonTree(int id, java.lang.String name, java.lang.String rank, AbstractNode p)
Creates a new instance of TaxonTree

Method Summary

protected void	addChild(AbstractNode n)
protected void	addS1Score(Score s)
protected void	addS2Score(Score s)
void	changeConfidence(SigCalculator cal) calculate the count of sequences assigned to the node, only count the sequence with score for that node greater or equal to confidence cutoff value
ComparisonBrowserNode	findNode(int id) returns a node with the given taxid if found.
(package private) TaxonTree	getChildbyTaxid(int taxid, java.lang.String name, java.lang.String rank) Given a assignment, first search the asigned node among the children, if the child does not exist, create a new child node.
java.util.Iterator	getDetailIterator(float conf)
(package private) AbstractNode	getFirstChild()
(package private) Score	getFirstS1Score()
(package private) Score	getFirstS2Score()
private Score	getLastS1Score()
private Score	getLastS2Score()
java.lang.String	getName()
java.lang.String	getRank()
int	getTaxid()
private void	setFirstS1Score(Score s)
private void	setFirstS2Score(Score s)

Methods inherited from class edu.msu.cme.rdp.classifier.comparison.AbstractNode

addSibling, getDoubleSignificance, getIndent, getLineageIterator, getNextSibling, getParent, getS1Count, getS2Count, getSignificance, getTaxonIterator, incS1Count, incS2Count, resetCount, setIndent, setParent, setSignificance

Methods inherited from class java.lang.Object

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

Field Detail

taxid

private int taxid

name

private java.lang.String name

rank

private java.lang.String rank

firstChild

private AbstractNode firstChild

firstS1Score

private Score firstS1Score

lastS1Score

private Score lastS1Score

firstS2Score

private Score firstS2Score

lastS2Score

private Score lastS2Score

Constructor Detail

TaxonTree

public TaxonTree(int id,
                 java.lang.String name,
                 java.lang.String rank,
                 AbstractNode p)

Creates a new instance of TaxonTree

Method Detail

getDetailIterator

public java.util.Iterator getDetailIterator(float conf)

Specified by:

getDetailIterator in interface ComparisonBrowserNode

Specified by:

getDetailIterator in class AbstractNode

getName

public java.lang.String getName()

Specified by:

getName in interface Taxon

Specified by:

getName in class AbstractNode

getRank

public java.lang.String getRank()

Specified by:

getRank in interface Taxon

Specified by:

getRank in class AbstractNode

getTaxid

public int getTaxid()

Specified by:

getTaxid in interface Taxon

Specified by:

getTaxid in class AbstractNode

getFirstChild

AbstractNode getFirstChild()

Specified by:

getFirstChild in class AbstractNode

getFirstS1Score

Score getFirstS1Score()

getFirstS2Score

Score getFirstS2Score()

getLastS1Score

private Score getLastS1Score()

getLastS2Score

private Score getLastS2Score()

addChild

protected void addChild(AbstractNode n)

setFirstS1Score

private void setFirstS1Score(Score s)

setFirstS2Score

private void setFirstS2Score(Score s)

addS1Score

protected void addS1Score(Score s)

addS2Score

protected void addS2Score(Score s)

getChildbyTaxid

TaxonTree getChildbyTaxid(int taxid,
                          java.lang.String name,
                          java.lang.String rank)

Given a assignment, first search the asigned node among the children, if the child does not exist, create a new child node.

changeConfidence

public void changeConfidence(SigCalculator cal)

calculate the count of sequences assigned to the node, only count the sequence with score for that node greater or equal to confidence cutoff value

Specified by:

changeConfidence in interface ComparisonBrowserNode

Specified by:

changeConfidence in class AbstractNode

findNode

public ComparisonBrowserNode findNode(int id)

returns a node with the given taxid if found. returns null if not found.

Specified by:

findNode in interface ComparisonBrowserNode

Specified by:

findNode in class AbstractNode