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

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
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.
java.util.Iterator	getDetailIterator(float conf)
java.lang.String	getName()
java.lang.String	getRank()
int	getTaxid()

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

getDoubleSignificance, getIndent, getLineageIterator, getS1Count, getS2Count, getSignificance, getTaxonIterator

Methods inherited from class java.lang.Object

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

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

addChild

protected void addChild(AbstractNode n)

addS1Score

protected void addS1Score(Score s)

addS2Score

protected void addS2Score(Score s)

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