uk.ac.man.entitytagger.entities.misc
Class CellLines

java.lang.Object
  uk.ac.man.entitytagger.entities.misc.CellLines

public class CellLines
extends java.lang.Object

This class will, given a CLKB CellLine database .owl file, parse its contents and output a tab-delimited regular expression file suitable for import by the automaton generating software. Using it, an automaton can be generated that may be used to locate and identify cell lines.

Author:

Martin Gerner

Constructor Summary

CellLines()

Method Summary

static void	main(java.lang.String[] args)
private static java.lang.String	match(java.lang.String organism, Matcher matcher)
private static org.w3c.dom.Node	parseXML(java.io.File file, java.lang.String[] dtdLocations)
private static void	run(org.w3c.dom.Node root, java.io.File outFile, Matcher matcher, java.util.logging.Logger logger, java.sql.Connection conn, java.lang.String table)
private static void	run2(org.w3c.dom.Node cl, java.sql.PreparedStatement pstmt, java.io.BufferedWriter outStream, Matcher matcher)
private static java.lang.String	toRegexp(java.lang.String name)

Methods inherited from class java.lang.Object

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

Constructor Detail

CellLines

public CellLines()

Method Detail

parseXML

private static org.w3c.dom.Node parseXML(java.io.File file,
                                         java.lang.String[] dtdLocations)

main

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

match

private static java.lang.String match(java.lang.String organism,
                                      Matcher matcher)

run

private static void run(org.w3c.dom.Node root,
                        java.io.File outFile,
                        Matcher matcher,
                        java.util.logging.Logger logger,
                        java.sql.Connection conn,
                        java.lang.String table)

run2

private static void run2(org.w3c.dom.Node cl,
                         java.sql.PreparedStatement pstmt,
                         java.io.BufferedWriter outStream,
                         Matcher matcher)

toRegexp

private static java.lang.String toRegexp(java.lang.String name)