MCTaxon

java.lang.Object

edu.msu.cme.rdp.taxatree.Node

edu.msu.cme.rdp.taxatree.Taxon

edu.msu.cme.rdp.multicompare.taxon.MCTaxon

Direct Known Subclasses:: UnifracTaxon

public class MCTaxon extends edu.msu.cme.rdp.taxatree.Taxon

Field Summary

Fields

Modifier and Type

Field

Description

static final int

Count_Array_size

protected Map<MCSample,double[]>

sampleCountMap

Fields inherited from class edu.msu.cme.rdp.taxatree.Taxon
ROOT_TAXON

Fields inherited from class edu.msu.cme.rdp.taxatree.Node
taxid
Constructor Summary

Constructors

Constructor

Description

MCTaxon(int id, String name, String rank)

MCTaxon(int id, String name, String rank, boolean unclassified)

MCTaxon(edu.msu.cme.rdp.taxatree.Taxon t)
Method Summary

Modifier and Type

Method

Description

void

addSequence(String seqid)

double

getCopyCorrectedCount(MCSample s)

double

getCount(MCSample s)

String

getLineage()

Set<MCSample>

getSamples()

Set<String>

getSequences()

void

incCount(MCSample s, double c)

void

incCount(MCSample s, double c, double copyNumber)

void

setLineage(String lineage)

Methods inherited from class edu.msu.cme.rdp.taxatree.Taxon
getName, getRank, getTaxid, getUnclassifiedId, isUnclassified

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- sampleCountMap
  
  protected Map<MCSample,double[]> sampleCountMap
- Count_Array_size
  
  public static final int Count_Array_size
  See Also:
  
  Constant Field Values
Constructor Details
- MCTaxon
  
  public MCTaxon(int id, String name, String rank)
- MCTaxon
  
  public MCTaxon(int id, String name, String rank, boolean unclassified)
- MCTaxon
  
  public MCTaxon(edu.msu.cme.rdp.taxatree.Taxon t)
Method Details
- addSequence
  
  public void addSequence(String seqid)
- getSequences
  
  public Set<String> getSequences()
- setLineage
  
  public void setLineage(String lineage)
- getLineage
  
  public String getLineage()
- getSamples
  
  public Set<MCSample> getSamples()
- getCount
  
  public double getCount(MCSample s)
- getCopyCorrectedCount
  
  public double getCopyCorrectedCount(MCSample s)
- incCount
  
  public void incCount(MCSample s, double c)
- incCount
  
  public void incCount(MCSample s, double c, double copyNumber)