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

Description

TaxonTree(int id, String name, String rank, AbstractNode p)

Creates a new instance of TaxonTree
Method Summary

Modifier and Type

Method

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.

Iterator

getDetailIterator(float conf)

String

getName()

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 Details
- TaxonTree
  
  public TaxonTree(int id, String name, String rank, AbstractNode p)
  
  Creates a new instance of TaxonTree
Method Details
- getDetailIterator
  
  public Iterator getDetailIterator(float conf)
  
  Specified by:
  
  getDetailIterator in interface ComparisonBrowserNode
  
  Specified by:
  
  getDetailIterator in class AbstractNode
- getName
  
  public String getName()
  
  Specified by:
  
  getName in interface Taxon
  
  Specified by:
  
  getName in class AbstractNode
- getRank
  
  public 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

Class TaxonTree

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Details

TaxonTree

Method Details

getDetailIterator

getName

getRank

getTaxid

addChild

addS1Score

addS2Score

changeConfidence

findNode