Class TaxonTree
java.lang.Object
edu.msu.cme.rdp.classifier.comparison.AbstractNode
edu.msu.cme.rdp.classifier.comparison.TaxonTree
- All Implemented Interfaces:
ComparisonBrowserNode
,Taxon
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Constructor Summary
ConstructorsConstructorDescriptionTaxonTree
(int id, String name, String rank, AbstractNode p) Creates a new instance of TaxonTree -
Method Summary
Modifier and TypeMethodDescriptionprotected void
protected void
addS1Score
(Score s) protected void
addS2Score
(Score s) void
calculate the count of sequences assigned to the node, only count the sequence with score for that node greater or equal to confidence cutoff valuefindNode
(int id) returns a node with the given taxid if found.getDetailIterator
(float conf) getName()
getRank()
int
getTaxid()
Methods inherited from class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getDoubleSignificance, getIndent, getLineageIterator, getS1Count, getS2Count, getSignificance, getTaxonIterator
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Constructor Details
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TaxonTree
Creates a new instance of TaxonTree
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Method Details
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getDetailIterator
- Specified by:
getDetailIterator
in interfaceComparisonBrowserNode
- Specified by:
getDetailIterator
in classAbstractNode
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getName
- Specified by:
getName
in interfaceTaxon
- Specified by:
getName
in classAbstractNode
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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
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addS1Score
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addS2Score
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changeConfidence
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
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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