seth

Class SETH

java.lang.Object

seth.SETH

public class SETH
extends Object

This class encapsulates modified MutationFinder, SETHNER, OldNomenclature, and dbSNPRecognizer. This allows to recognize SNPs written in the latest HGVS nomenclature (e.g. p.Ala123Tyr), SNPs written in free text (e.g. Ala to Tyr substitution at position 123), SNPs written in deprecated nomenclature and dbSNP mentions

Author:

Philippe Thomas

Constructor Summary

Constructors

Constructor and Description
SETH() Parameter free constructor for SETH.
SETH(String regexFile, boolean exactGrammar, boolean oldNomenclature) Initializes MutationFinder and SETHNER.

Method Summary

Modifier and Type	Method and Description
List<MutationMention>	findMutations(String text) Searches for mutation mentions in applied text and returns them
static void	main(String[] args) Minimal example to perform named entity recognition and normalization using SETH

Methods inherited from class java.lang.Object

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

Constructor Detail

SETH

public SETH()

Parameter free constructor for SETH. This constructor initializes SETH with reasonable default settings. The constructor SETH(String, boolean, boolean) provides more flexibility for advanced configuration MutationFinder is initialized using the regular expressions contained in Java-Archive 'resources/mutations.txt' SETH-NER (HGVS) is initialized with fuzzy match-option

SETH

public SETH(String regexFile,
            boolean exactGrammar,
            boolean oldNomenclature)

Initializes MutationFinder and SETHNER. Requires a file with regular expressions for MutationFinder

Parameters:

regexFile - File location with regular expressions for MutationFinder

exactGrammar - If true, SETH uses the exact EBNF grammar, otherwise matching is fuzzy

oldNomenclature - If true, SETH searches for deletions, insertions, frameshifts in old nomenclature

Method Detail

findMutations

public List<MutationMention> findMutations(String text)

Searches for mutation mentions in applied text and returns them

Parameters:

text - Text possibly containing a mutation mention

Returns:

List of MutationMention

main

public static void main(String[] args)
                 throws SQLException,
                        IOException

Minimal example to perform named entity recognition and normalization using SETH

Parameters:

args -

Throws:

SQLException

IOException