edu.msu.cme.rdp.classifier.train

Class TreeFactory

java.lang.Object

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

public class TreeFactory
extends java.lang.Object

A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.

Constructor Summary

Constructors

Constructor and Description
TreeFactory(java.io.Reader taxReader, int trainsetNo, java.lang.String version, java.lang.String modification) Creates new TreeFactory.

Method Summary

Methods

Modifier and Type	Method and Description
RawHierarchyTree	getRoot() Gets the root of the tree
void	parseCopyNumberFile(java.lang.String cnFile) parse the copy number file first step, take the copy number info from the lowest rank taxa, then calculate the copy number of the parent taxa based on the immediate children second step, for any taxon without copy number info, uses the
void	parseSequenceFile(LineageSequenceParser parser)

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,
           int trainsetNo,
           java.lang.String version,
           java.lang.String modification)
            throws java.io.IOException,
                   NameRankDupException

Creates new TreeFactory.

Throws:

java.io.IOException

NameRankDupException

Method Detail

parseSequenceFile

public void parseSequenceFile(LineageSequenceParser parser)
                       throws java.io.IOException

Throws:

java.io.IOException

parseCopyNumberFile

public void parseCopyNumberFile(java.lang.String cnFile)
                         throws java.io.IOException

parse the copy number file first step, take the copy number info from the lowest rank taxa, then calculate the copy number of the parent taxa based on the immediate children second step, for any taxon without copy number info, uses the

Parameters:

cnFile -

Throws:

java.io.IOException

getRoot

public RawHierarchyTree getRoot()

Gets the root of the tree