Package edu.msu.cme.rdp.classifier.train.validation

Class HierarchyTree

java.lang.Object

edu.msu.cme.rdp.classifier.train.validation.HierarchyTree

public class HierarchyTree
extends java.lang.Object

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	changeParentSeqCount(int i)
void	createWordOccurrenceFromSubclasses()	creates the word occurrence array from its children if the word occurrence for this node does not exist
java.util.Collection	getLeaves()	Gets the array of Sequenceleaves if any
int	getMissCount()
java.lang.String	getName()	Gets the name of the treenode
void	getNodeList(java.lang.String level, java.util.List nodeList)	get all the lowest level nodes in given hierarchy level starting from the given root
void	getNodeMap(java.lang.String level, java.util.HashMap<java.lang.String,HierarchyTree> nodeMap)	get all the lowest level nodes in given hierarchy level starting from the given root
int	getNumberofUniqueWords()
int	getNumOfLeaves()	Counts the number of sequence leaves below this tree
int	getNumTotalTestedseq()
HierarchyTree	getParent()	Gets the parent treenode
int	getSizeofChildren()	Gets the size of the children
int	getSizeofLeaves()	Gets the size of sequence leaves directly belong to this tree, not including the hidden leaves
int	getSizeofSubclasses()	Gets the size of the subclasses
HierarchyTree	getSubclassbyName(java.lang.String n)	Gets the subclass with the given name
java.util.Collection<HierarchyTree>	getSubclasses()	Gets the array of the subclasses if any
Taxonomy	getTaxonomy()
int	getTotalSeqs()
int	getWordOccurrence(int wordIndex)	Gets the word occurrence for the given word index
int	getWordOccurrenceSize()
void	hideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)	This method hides a sequence by removing the words of that sequence from the total wordOccurrence
void	incMissCount()
void	incNumTotalTestedseq()
void	increTotalSeqs()
void	initWordOccurrence(LineageSequence pSeq, float[] wordPriorArr, boolean initWordOccurrence)	This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
boolean	isSingleton()
boolean	isWordOccurDone()
void	unhideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)	This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree

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,
                     HierarchyTree p,
                     Taxonomy tax)

Creates new HierarchyTree given the name and its parent

Method Detail

getName

public java.lang.String getName()

Gets the name of the treenode

getParent

public HierarchyTree getParent()

Gets the parent treenode

getSubclasses

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

Gets the array of the subclasses if any

getLeaves

public java.util.Collection getLeaves()

Gets the array of Sequenceleaves if any

getSubclassbyName

public HierarchyTree getSubclassbyName(java.lang.String n)

Gets the subclass with the given name

getSizeofChildren

public int getSizeofChildren()

Gets the size of the children

getSizeofSubclasses

public int getSizeofSubclasses()

Gets the size of the subclasses

getSizeofLeaves

public int getSizeofLeaves()

Gets the size of sequence leaves directly belong to this tree, not including the hidden leaves

initWordOccurrence

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

This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree

Throws:

java.io.IOException

unhideSeq

public void unhideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)
               throws java.io.IOException

This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree

Throws:

java.io.IOException

hideSeq

public void hideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)
             throws java.io.IOException

This method hides a sequence by removing the words of that sequence from the total wordOccurrence

Throws:

java.io.IOException

changeParentSeqCount

public void changeParentSeqCount(int i)

isWordOccurDone

public boolean isWordOccurDone()

getWordOccurrenceSize

public int getWordOccurrenceSize()

getNumberofUniqueWords

public int getNumberofUniqueWords()

createWordOccurrenceFromSubclasses

public void createWordOccurrenceFromSubclasses()

creates the word occurrence array from its children if the word occurrence for this node does not exist

getWordOccurrence

public int getWordOccurrence(int wordIndex)

Gets the word occurrence for the given word index

getNumOfLeaves

public int getNumOfLeaves()

Counts the number of sequence leaves below this tree

increTotalSeqs

public void increTotalSeqs()

getTotalSeqs

public int getTotalSeqs()

getMissCount

public int getMissCount()

getNumTotalTestedseq

public int getNumTotalTestedseq()

incNumTotalTestedseq

public void incNumTotalTestedseq()

incMissCount

public void incMissCount()

getTaxonomy

public Taxonomy getTaxonomy()

isSingleton

public boolean isSingleton()

getNodeList

public void getNodeList(java.lang.String level,
                        java.util.List nodeList)

get all the lowest level nodes in given hierarchy level starting from the given root

getNodeMap

public void getNodeMap(java.lang.String level,
                       java.util.HashMap<java.lang.String,HierarchyTree> nodeMap)

get all the lowest level nodes in given hierarchy level starting from the given root