edu.msu.cme.rdp.classifier.rrnaclassifier
Class HierarchyTree

java.lang.Object
  edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree

public class HierarchyTree
extends java.lang.Object

A HierarchyTree holds the taxonomic information of a taxon.

Field Summary

private int	genusIndex -1 means not a genus node.
private int	leaveCount
private java.lang.String	name
private HierarchyTree	parent
private java.lang.String	rank
private java.util.List	subclasses
private int	taxid

Constructor Summary

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

Method Summary

(package private) void	addParent(HierarchyTree p) Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.
private void	addSubclass(HierarchyTree c) Adds a child treenode to subclass.
(package private) int	getGenusIndex() Gets the index of the genus treenode in the genusNodeList.
(package private) int	getLeaveCount() Gets the size of sequence leaves directly belong to this treenode.
java.lang.String	getName() Gets the name of the treenode.
(package private) HierarchyTree	getParent() Gets the parent treenode.
java.lang.String	getRank() Gets the rank of the treenode.
(package private) int	getSizeofSubclasses() Gets the list of the child treenodes.
java.util.List	getSubclasses() Gets the name of the treenode.
int	getTaxid() Gets the taxon id of the treenode.

Methods inherited from class java.lang.Object

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

Field Detail

name

private java.lang.String name

rank

private java.lang.String rank

taxid

private int taxid

leaveCount

private int leaveCount

parent

private HierarchyTree parent

subclasses

private java.util.List subclasses

genusIndex

private int genusIndex

-1 means not a genus node. If this node is a genus node, the genusIndex indicates the index of this node among all the genera

Constructor Detail

HierarchyTree

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

Creates new HierarchyTree given the taxonomic information.

Method Detail

addParent

void addParent(HierarchyTree p)

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

addSubclass

private void addSubclass(HierarchyTree c)

Adds a child treenode to subclass.

getName

public java.lang.String getName()

Gets the name of the treenode.

getParent

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 getSubclasses()

Gets the name of the treenode.

getSizeofSubclasses

int getSizeofSubclasses()

Gets the list of the child treenodes.

getLeaveCount

int getLeaveCount()

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

getGenusIndex

int getGenusIndex()

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