Class TaxonTree
- java.lang.Object
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- edu.msu.cme.rdp.classifier.comparison.AbstractNode
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- edu.msu.cme.rdp.classifier.comparison.TaxonTree
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- All Implemented Interfaces:
ComparisonBrowserNode
,Taxon
public class TaxonTree extends AbstractNode
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Constructor Summary
Constructors Constructor Description TaxonTree(int id, java.lang.String name, java.lang.String rank, AbstractNode p)
Creates a new instance of TaxonTree
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Method Summary
All Methods Instance Methods Concrete Methods 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 valueComparisonBrowserNode
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()
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Methods inherited from class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getDoubleSignificance, getIndent, getLineageIterator, getS1Count, getS2Count, getSignificance, getTaxonIterator
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Constructor Detail
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TaxonTree
public TaxonTree(int id, java.lang.String name, java.lang.String rank, AbstractNode p)
Creates a new instance of TaxonTree
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Method Detail
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getDetailIterator
public java.util.Iterator getDetailIterator(float conf)
- Specified by:
getDetailIterator
in interfaceComparisonBrowserNode
- Specified by:
getDetailIterator
in classAbstractNode
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getName
public java.lang.String getName()
- Specified by:
getName
in interfaceTaxon
- Specified by:
getName
in classAbstractNode
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getRank
public java.lang.String getRank()
- Specified by:
getRank
in interfaceTaxon
- Specified by:
getRank
in classAbstractNode
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getTaxid
public int getTaxid()
- Specified by:
getTaxid
in interfaceTaxon
- Specified by:
getTaxid
in classAbstractNode
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addChild
protected void addChild(AbstractNode n)
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addS1Score
protected void addS1Score(Score s)
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addS2Score
protected void addS2Score(Score s)
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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 interfaceComparisonBrowserNode
- Specified by:
changeConfidence
in classAbstractNode
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findNode
public ComparisonBrowserNode findNode(int id)
returns a node with the given taxid if found. returns null if not found.- Specified by:
findNode
in interfaceComparisonBrowserNode
- Specified by:
findNode
in classAbstractNode
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