edu.msu.cme.rdp.classifier.comparison
Class TaxonTree
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 |
TaxonTree(int id,
java.lang.String name,
java.lang.String rank,
AbstractNode p)
Creates a new instance of TaxonTree |
| Methods inherited from class edu.msu.cme.rdp.classifier.comparison.AbstractNode |
addSibling, getDoubleSignificance, getIndent, getLineageIterator, getNextSibling, getParent, getS1Count, getS2Count, getSignificance, getTaxonIterator, incS1Count, incS2Count, resetCount, setIndent, setParent, setSignificance |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
taxid
private int taxid
name
private java.lang.String name
rank
private java.lang.String rank
firstChild
private AbstractNode firstChild
firstS1Score
private Score firstS1Score
lastS1Score
private Score lastS1Score
firstS2Score
private Score firstS2Score
lastS2Score
private Score lastS2Score
TaxonTree
public TaxonTree(int id,
java.lang.String name,
java.lang.String rank,
AbstractNode p)
- Creates a new instance of TaxonTree
getDetailIterator
public java.util.Iterator getDetailIterator(float conf)
- Specified by:
getDetailIterator in interface ComparisonBrowserNode- Specified by:
getDetailIterator in class AbstractNode
getName
public java.lang.String getName()
- Specified by:
getName in interface Taxon- Specified by:
getName in class AbstractNode
getRank
public java.lang.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
getFirstChild
AbstractNode getFirstChild()
- Specified by:
getFirstChild in class AbstractNode
getFirstS1Score
Score getFirstS1Score()
getFirstS2Score
Score getFirstS2Score()
getLastS1Score
private Score getLastS1Score()
getLastS2Score
private Score getLastS2Score()
addChild
protected void addChild(AbstractNode n)
setFirstS1Score
private void setFirstS1Score(Score s)
setFirstS2Score
private void setFirstS2Score(Score s)
addS1Score
protected void addS1Score(Score s)
addS2Score
protected void addS2Score(Score s)
getChildbyTaxid
TaxonTree getChildbyTaxid(int taxid,
java.lang.String name,
java.lang.String rank)
- Given a assignment, first search the asigned node among the children,
if the child does not exist, create a new child node.
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