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

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

All Implemented Interfaces:

ComparisonBrowserNode, Taxon

Direct Known Subclasses:

TaxonTree, UncNode

public abstract class AbstractNode
extends java.lang.Object
implements Taxon, ComparisonBrowserNode

Nested Class Summary

(package private) class	AbstractNode.LineageIterator An Iterator of the ancestor nodes of the current node(not included) returns the most recent ancestor last.
(package private) class	AbstractNode.TaxonIterator An Iterator of the BrowserNode.

Field Summary

private static java.text.DecimalFormat	df
private int	indent
private AbstractNode	nextSibling
private AbstractNode	parent
private int	s1Count
private int	s2Count
private double	significance

Constructor Summary

AbstractNode()
Creates a new instance of AbstractNode

Method Summary

(package private) void	addSibling(AbstractNode n)
abstract void	changeConfidence(SigCalculator cal)
abstract ComparisonBrowserNode	findNode(int id)
abstract java.util.Iterator	getDetailIterator(float conf)
double	getDoubleSignificance()
(package private) abstract AbstractNode	getFirstChild()
int	getIndent()
java.util.Iterator	getLineageIterator()
abstract java.lang.String	getName()
(package private) AbstractNode	getNextSibling()
(package private) AbstractNode	getParent() the parent of the root is null
abstract java.lang.String	getRank()
int	getS1Count()
int	getS2Count()
java.lang.String	getSignificance()
abstract int	getTaxid()
java.util.Iterator	getTaxonIterator(int depth)
(package private) void	incS1Count(int c)
(package private) void	incS2Count(int c)
(package private) void	resetCount()
(package private) void	setIndent(int d)
(package private) void	setParent(AbstractNode n)
(package private) void	setSignificance(double s)

Methods inherited from class java.lang.Object

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

Field Detail

df

private static java.text.DecimalFormat df

indent

private int indent

parent

private AbstractNode parent

nextSibling

private AbstractNode nextSibling

s1Count

private int s1Count

s2Count

private int s2Count

significance

private double significance

Constructor Detail

AbstractNode

public AbstractNode()

Creates a new instance of AbstractNode

Method Detail

getTaxonIterator

public java.util.Iterator getTaxonIterator(int depth)

Specified by:

getTaxonIterator in interface ComparisonBrowserNode

getLineageIterator

public java.util.Iterator getLineageIterator()

Specified by:

getLineageIterator in interface ComparisonBrowserNode

getDetailIterator

public abstract java.util.Iterator getDetailIterator(float conf)

Specified by:

getDetailIterator in interface ComparisonBrowserNode

changeConfidence

public abstract void changeConfidence(SigCalculator cal)

Specified by:

changeConfidence in interface ComparisonBrowserNode

getFirstChild

abstract AbstractNode getFirstChild()

findNode

public abstract ComparisonBrowserNode findNode(int id)

Specified by:

findNode in interface ComparisonBrowserNode

getName

public abstract java.lang.String getName()

Specified by:

getName in interface Taxon

getRank

public abstract java.lang.String getRank()

Specified by:

getRank in interface Taxon

getTaxid

public abstract int getTaxid()

Specified by:

getTaxid in interface Taxon

getParent

AbstractNode getParent()

the parent of the root is null

getNextSibling

AbstractNode getNextSibling()

getS1Count

public int getS1Count()

Specified by:

getS1Count in interface Taxon

getS2Count

public int getS2Count()

Specified by:

getS2Count in interface Taxon

getDoubleSignificance

public double getDoubleSignificance()

getSignificance

public java.lang.String getSignificance()

Specified by:

getSignificance in interface Taxon

getIndent

public int getIndent()

Specified by:

getIndent in interface Taxon

incS1Count

void incS1Count(int c)

incS2Count

void incS2Count(int c)

resetCount

void resetCount()

setParent

void setParent(AbstractNode n)

setIndent

void setIndent(int d)

setSignificance

void setSignificance(double s)

addSibling

void addSibling(AbstractNode n)