edu.msu.cme.rdp.classifier.train
Class RawHierarchyTree

java.lang.Object
  edu.msu.cme.rdp.classifier.train.RawHierarchyTree

public class RawHierarchyTree
extends java.lang.Object

A RawHierarchyTree holds the raw taxon and sequences information. A RawHierarchyTree can only have one type of children: child treenodes or child sequences.

Field Summary

private int	genusIndex
private int	leaveCount
private java.lang.String	name
private RawHierarchyTree	parent
private java.util.Map	subclasses
private Taxonomy	taxon
private int[]	wordOccurrence

Constructor Summary

RawHierarchyTree(java.lang.String n, RawHierarchyTree p, Taxonomy tax)
Creates new RawHierarchyTree given the name and its parent.

Method Summary

private void	addParent(RawHierarchyTree p) Adds the parent HierarchyTree, also adds this node to the parent tree as a child.
private void	addSubclass(RawHierarchyTree c) Adds a child treenode.
int	getGenusIndex() Returns the genus index of this treenode.
int	getLeaveCount() Counts the number of sequence leaves below this tree.
java.lang.String	getName() Gets the name of the treenode.
int	getNonSingletonLeaveCount() Counts the number of non-singleton sequence leaves below this tree.
RawHierarchyTree	getParent() Gets the parent treenode.
int	getSizeofChildren() Gets the size of the children, either taxon children or sequence leaves.
int	getSizeofSubclasses() Gets the size of the child treenodes.
RawHierarchyTree	getSubclassbyName(java.lang.String n) Gets the child treenode with the given name.
java.util.Collection	getSubclasses() Gets the array of the subclasses if any.
Taxonomy	getTaxonomy() Returns the taxon object of this treenode.
int	getWordOccurrence(int wordIndex) Gets the word occurrence for the given word index.
int	getWordOccurrenceSize() Returns the size of the array wordOccurrence.
void	initWordOccurrence(ParsedRawSequence pSeq, float[] wordPriorArr) This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree.
boolean	isSingleton()
private boolean	isWordExist(int[] wordList, int wordIndex) Checks if this word already been added to the wordOccurrence.
void	releaseWordOccurrence() Resets the array wordOccurrence to null.
void	setGenusIndex(int i) Sets the genus index of this 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

leaveCount

private int leaveCount

parent

private RawHierarchyTree parent

subclasses

private java.util.Map subclasses

wordOccurrence

private int[] wordOccurrence

taxon

private Taxonomy taxon

genusIndex

private int genusIndex

Constructor Detail

RawHierarchyTree

public RawHierarchyTree(java.lang.String n,
                        RawHierarchyTree p,
                        Taxonomy tax)

Creates new RawHierarchyTree given the name and its parent. Note: a RawHierarchyTree can only have one type of children: child treenodes or child sequences. Usually the lowest ranked nodes contain the sequence leaves.

Method Detail

addParent

private void addParent(RawHierarchyTree p)

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

addSubclass

private void addSubclass(RawHierarchyTree c)

Adds a child treenode.

getName

public java.lang.String getName()

Gets the name of the treenode.

getParent

public RawHierarchyTree getParent()

Gets the parent treenode.

getSubclasses

public java.util.Collection getSubclasses()

Gets the array of the subclasses if any.

getSubclassbyName

public RawHierarchyTree getSubclassbyName(java.lang.String n)

Gets the child treenode with the given name.

getSizeofChildren

public int getSizeofChildren()

Gets the size of the children, either taxon children or sequence leaves.

getSizeofSubclasses

public int getSizeofSubclasses()

Gets the size of the child treenodes.

initWordOccurrence

public void initWordOccurrence(ParsedRawSequence pSeq,
                               float[] wordPriorArr)
                        throws java.io.IOException

This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree. Duplicate words from one sequence will be count only once.

Throws:

java.io.IOException

isWordExist

private boolean isWordExist(int[] wordList,
                            int wordIndex)

Checks if this word already been added to the wordOccurrence. Returns true if found.

getWordOccurrenceSize

public int getWordOccurrenceSize()

Returns the size of the array wordOccurrence.

getWordOccurrence

public int getWordOccurrence(int wordIndex)

Gets the word occurrence for the given word index.

releaseWordOccurrence

public void releaseWordOccurrence()

Resets the array wordOccurrence to null.

getLeaveCount

public int getLeaveCount()

Counts the number of sequence leaves below this tree.

isSingleton

public boolean isSingleton()

getNonSingletonLeaveCount

public int getNonSingletonLeaveCount()

Counts the number of non-singleton sequence leaves below this tree.

getTaxonomy

public Taxonomy getTaxonomy()

Returns the taxon object of this treenode.

setGenusIndex

public void setGenusIndex(int i)

Sets the genus index of this treenode.

getGenusIndex

public int getGenusIndex()

Returns the genus index of this treenode.