Package de.julielab.jules.ae.genemapping.resources

Class SynonymIndexGenerator

java.lang.Object

de.julielab.jules.ae.genemapping.resources.SynonymIndexGenerator

public class SynonymIndexGenerator
extends java.lang.Object

Constructor Summary

Constructors

Constructor	Description
SynonymIndexGenerator(java.io.File dictFile, java.io.File indexFile)

Method Summary

Modifier and Type	Method	Description
void	createIndex()	create the index, i.e.
static void	main(java.lang.String[] args)	To execute the ContextIndexGenerator start it with the following command-line arguments: arg0: path to resources directory arg1: path to synonym indices directory

Methods inherited from class java.lang.Object

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

Constructor Detail

SynonymIndexGenerator

public SynonymIndexGenerator(java.io.File dictFile,
                             java.io.File indexFile)
                      throws java.io.FileNotFoundException,
                             java.io.IOException

Parameters:

dictFile - A file containing gene or protein names / synonyms and their respective NCBI Gene or UniProt ID. No term normalization is expected for this dictionary.

indexFile - The directory where the name / synonym index will be written to.

Throws:

java.io.FileNotFoundException

java.io.IOException

Method Detail

main

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

To execute the ContextIndexGenerator start it with the following command-line arguments:
arg0: path to resources directory arg1: path to synonym indices directory

Parameters:

args -

createIndex

public void createIndex()
                 throws java.io.IOException

create the index, i.e. read from the biothesaurus file (which is expected to have normalized synonyms!) and then write it to the index.

Throws:

java.io.IOException