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

java.lang.Object
  org.xml.sax.helpers.DefaultHandler
      edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

 class TreeFileParser
extends org.xml.sax.helpers.DefaultHandler

A parser to parse a reader containing taxonomic training information. Note: The first TreeNode is the root TreeNode.

Field Summary

private HierarchyTree	root
private java.util.Stack	treeNodeStack

Constructor Summary

TreeFileParser()
Creates a new instance of TreeFileParser.

Method Summary

(package private) HierarchyTree	createTree(java.io.Reader in, HierarchyVersion version) Reads from a reader that contains the information for each treenode.
void	endElement(java.lang.String str, java.lang.String str1, java.lang.String str2)
void	error(org.xml.sax.SAXParseException e)
private void	load(java.lang.String document)
void	startElement(java.lang.String namespaceURI, java.lang.String lName, java.lang.String qName, org.xml.sax.Attributes attrs)

Methods inherited from class org.xml.sax.helpers.DefaultHandler

characters, endDocument, endPrefixMapping, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Field Detail

treeNodeStack

private java.util.Stack treeNodeStack

root

private HierarchyTree root

Constructor Detail

TreeFileParser

TreeFileParser()

Creates a new instance of TreeFileParser.

Method Detail

createTree

HierarchyTree createTree(java.io.Reader in,
                         HierarchyVersion version)
                   throws java.io.IOException,
                          TrainingDataException

Reads from a reader that contains the information for each treenode. Creates all the HierarchyTrees and returns the root of the trees. Note: The first TreeNode is the root TreeNode. The version information should be obtained from the other files first.

Throws:

java.io.IOException

TrainingDataException

load

private void load(java.lang.String document)
           throws TrainingDataException,
                  java.io.IOException

Throws:

TrainingDataException

java.io.IOException

startElement

public void startElement(java.lang.String namespaceURI,
                         java.lang.String lName,
                         java.lang.String qName,
                         org.xml.sax.Attributes attrs)
                  throws org.xml.sax.SAXException

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException

endElement

public void endElement(java.lang.String str,
                       java.lang.String str1,
                       java.lang.String str2)
                throws org.xml.sax.SAXException

Specified by:

endElement in interface org.xml.sax.ContentHandler

Overrides:

endElement in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException

error

public void error(org.xml.sax.SAXParseException e)
           throws org.xml.sax.SAXException

Specified by:

error in interface org.xml.sax.ErrorHandler

Overrides:

error in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException