Package edu.msu.cme.rdp.classifier

Class HierarchyTree

java.lang.Object

edu.msu.cme.rdp.classifier.HierarchyTree

public class HierarchyTree
extends java.lang.Object

A HierarchyTree holds the taxonomic information of a taxon.

Constructor Summary

Constructors

Constructor	Description
HierarchyTree(java.lang.String n, int taxid, java.lang.String rank, int leaves, int gIndex)
HierarchyTree(java.lang.String n, int taxid, java.lang.String rank, int leaves, int gIndex, double copyNumber)	Creates new HierarchyTree given the taxonomic information.

Method Summary

Modifier and Type	Method	Description
void	addParent(HierarchyTree p)	Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.
HierarchyTree	getChild(java.lang.String name)
double	getCopyNumber()
int	getGenusIndex()	Gets the index of the genus treenode in the genusNodeList.
int	getLeaveCount()	Gets the size of sequence leaves directly belong to this treenode.
java.lang.String	getName()	Gets the name of the treenode.
HierarchyTree	getParent()	Gets the parent treenode.
java.lang.String	getRank()	Gets the rank of the treenode.
int	getSizeofSubclasses()	Gets the list of the child treenodes.
java.util.List<HierarchyTree>	getSubclasses()	Gets the name of the treenode.
int	getTaxid()	Gets the taxon id of the treenode.
boolean	hasCopyNumberInfo()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HierarchyTree

public HierarchyTree(java.lang.String n,
                     int taxid,
                     java.lang.String rank,
                     int leaves,
                     int gIndex,
                     double copyNumber)

Creates new HierarchyTree given the taxonomic information.

HierarchyTree

public HierarchyTree(java.lang.String n,
                     int taxid,
                     java.lang.String rank,
                     int leaves,
                     int gIndex)

Method Detail

addParent

public void addParent(HierarchyTree p)

Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.

getName

public java.lang.String getName()

Gets the name of the treenode.

getParent

public HierarchyTree getParent()

Gets the parent treenode.

getRank

public java.lang.String getRank()

Gets the rank of the treenode.

getTaxid

public int getTaxid()

Gets the taxon id of the treenode.

getSubclasses

public java.util.List<HierarchyTree> getSubclasses()

Gets the name of the treenode.

getSizeofSubclasses

public int getSizeofSubclasses()

Gets the list of the child treenodes.

getChild

public HierarchyTree getChild(java.lang.String name)

getLeaveCount

public int getLeaveCount()

Gets the size of sequence leaves directly belong to this treenode.

getGenusIndex

public int getGenusIndex()

Gets the index of the genus treenode in the genusNodeList. Returns -1 if not a genus node.

getCopyNumber

public double getCopyNumber()

hasCopyNumberInfo

public boolean hasCopyNumberInfo()

Returns:

true if the taxon has copy number information