edu.msu.cme.rdp.classifier.io

Class TreeFileParser

java.lang.Object

org.xml.sax.helpers.DefaultHandler

edu.msu.cme.rdp.classifier.io.TreeFileParser

All Implemented Interfaces:

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

public 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.

Constructor Summary

Constructors

Constructor and Description
TreeFileParser() Creates a new instance of TreeFileParser.

Method Summary

Methods

Modifier and Type	Method and Description
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)
java.lang.String	getTrainRank()
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

Constructor Detail

TreeFileParser

public TreeFileParser()

Creates a new instance of TreeFileParser.

Method Detail

getTrainRank

public java.lang.String getTrainRank()

createTree

public 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

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