edu.uconn.mcb.lineageevolver.parsing
Class LECParser

java.lang.Object
  edu.uconn.mcb.lineageevolver.parsing.LECParser

public class LECParser

extends java.lang.Object

Parser for the XML-formatted ELECT output files.

Author:

Hasan Khalil

Field Summary

(package private) javax.xml.parsers.DocumentBuilder

_parser The actual parser used to parse the XML document.

Constructor Summary

LECParser()
Defualt constructor for objects of type LECParser.

Method Summary

static void	main(java.lang.String[] args) Test driver.
Configuration	parseFile(java.lang.String fileName) Parses an ELECT-generated XML file, yeilding a filled Configuration object.

Methods inherited from class java.lang.Object

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

Field Detail

_parser

javax.xml.parsers.DocumentBuilder _parser

The actual parser used to parse the XML document.

Constructor Detail

LECParser

public LECParser()
          throws javax.xml.parsers.ParserConfigurationException

Defualt constructor for objects of type LECParser. Generates all of the generic parser-oriented objects, and configures them to be ready for XML parsing.

Throws:

javax.xml.parsers.ParserConfigurationException - If there was an error with the backend XML parser.

Method Detail

parseFile

public Configuration parseFile(java.lang.String fileName)
                        throws java.io.IOException,
                               org.xml.sax.SAXException,
                               javax.xml.parsers.ParserConfigurationException

Parses an ELECT-generated XML file, yeilding a filled Configuration object. Uses the SAX2 XML parsing back-end to do all the dirty-work.

Parameters:

fileName - The filename of the XML file to parse.

Returns:

a Configuration containing the information from the provided XML file.

Throws:

java.io.IOException - If there was a problem with file I/O.

org.xml.sax.SAXException - If there was a problem with the XML parser backend.

javax.xml.parsers.ParserConfigurationException - If there was a problem obtaining a proper XML parser.

main

public static void main(java.lang.String[] args)

Test driver. Attempts to parse the file specified by the first argument and outputs the root genome found.

Parameters:

args - should be an array containing one item: the path to the file to be parsed.