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

Class TreeFactory

java.lang.Object

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

public class TreeFactory
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
TreeFactory(java.io.Reader taxReader) Creates new TreeFactory

Method Summary

Modifier and Type	Method and Description
HierarchyTree	addSequence(LineageSequence pSeq) For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent.
HierarchyTree	addSequence(LineageSequence pSeq, boolean initWordOccurrence)
void	buildTree() build the taxonomic tree without sequences attached to it
void	calculateWordPrior()
void	displayTreePhylo(HierarchyTree root, java.lang.String index, int indent) display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the description
java.lang.String	getLowestRank()
java.util.Set<java.lang.String>	getRankSet()
HierarchyTree	getRoot() Gets the root of the tree
Taxonomy	getTaxonomy(java.lang.String seqName, java.lang.String ancestorName, int pid, int index)
float	getWordPrior(int wordIndex)
void	printWordPriors()

Methods inherited from class java.lang.Object

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

Constructor Detail

TreeFactory

public TreeFactory(java.io.Reader taxReader)
            throws java.io.IOException

Creates new TreeFactory

Throws:

java.io.IOException

Method Detail

buildTree

public void buildTree()

build the taxonomic tree without sequences attached to it

addSequence

public HierarchyTree addSequence(LineageSequence pSeq)
                          throws java.io.IOException

For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent. If the root is already exist, checks the ParsedSequence to see if its oldest ancestor is the same as the previous root.

Throws:

java.io.IOException

addSequence

public HierarchyTree addSequence(LineageSequence pSeq,
                                 boolean initWordOccurrence)
                          throws java.io.IOException

Throws:

java.io.IOException

getTaxonomy

public Taxonomy getTaxonomy(java.lang.String seqName,
                            java.lang.String ancestorName,
                            int pid,
                            int index)

getRoot

public HierarchyTree getRoot()

Gets the root of the tree

getRankSet

public java.util.Set<java.lang.String> getRankSet()

getLowestRank

public java.lang.String getLowestRank()

displayTreePhylo

public void displayTreePhylo(HierarchyTree root,
                             java.lang.String index,
                             int indent)

display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the description

calculateWordPrior

public void calculateWordPrior()

printWordPriors

public void printWordPriors()
                     throws java.io.IOException

Throws:

java.io.IOException

getWordPrior

public float getWordPrior(int wordIndex)