public class MCTaxon
extends edu.msu.cme.rdp.taxatree.Taxon
Modifier and Type | Field and Description |
---|---|
static int |
Count_Array_size |
protected java.util.Map<MCSample,double[]> |
sampleCountMap |
Constructor and Description |
---|
MCTaxon(int id,
java.lang.String name,
java.lang.String rank) |
MCTaxon(int id,
java.lang.String name,
java.lang.String rank,
boolean unclassified) |
MCTaxon(edu.msu.cme.rdp.taxatree.Taxon t) |
Modifier and Type | Method and Description |
---|---|
void |
addSequence(java.lang.String seqid) |
double |
getCopyCorrectedCount(MCSample s) |
double |
getCount(MCSample s) |
java.lang.String |
getLineage() |
java.util.Set<MCSample> |
getSamples() |
java.util.Set<java.lang.String> |
getSequences() |
void |
incCount(MCSample s,
double c) |
void |
incCount(MCSample s,
double c,
double copyNumber) |
void |
setLineage(java.lang.String lineage) |
protected java.util.Map<MCSample,double[]> sampleCountMap
public static final int Count_Array_size
public MCTaxon(int id, java.lang.String name, java.lang.String rank)
public MCTaxon(int id, java.lang.String name, java.lang.String rank, boolean unclassified)
public MCTaxon(edu.msu.cme.rdp.taxatree.Taxon t)
public void addSequence(java.lang.String seqid)
public java.util.Set<java.lang.String> getSequences()
public void setLineage(java.lang.String lineage)
public java.lang.String getLineage()
public java.util.Set<MCSample> getSamples()
public double getCount(MCSample s)
public double getCopyCorrectedCount(MCSample s)
public void incCount(MCSample s, double c)
public void incCount(MCSample s, double c, double copyNumber)