Uses of Class
de.hu.berlin.wbi.objects.MutationMention

Packages that use MutationMention

Package	Description
cnveth	Package for copy number variation detection of genes (e.g., Aplification of BRCA1) Currently, this package is not used by SETH
de.hu.berlin.wbi.objects	Package with the main data objects.
seth	Package contains most logic of SETH
seth.ner.wrapper	Java wrapper for accessing the scala part of SETH (aka SETH-NER) SETH-NER performs Named Entity Recognition of variation mentions in the latest HGVS nomenclature based on a Backus Naur grammar

Uses of MutationMention in cnveth

Methods in cnveth that return types with arguments of type MutationMention

Modifier and Type	Method and Description
List<MutationMention>	CNVRecognizer.extractMutations(String text)
Set<MutationMention>	CNVETH.findMutations(String text) Extract mentions of CNV keywords and assigns Type CNV

Uses of MutationMention in de.hu.berlin.wbi.objects

Subclasses of MutationMention in de.hu.berlin.wbi.objects

Modifier and Type	Class and Description
class	MutationValidation This object represents a MutationMention from the validation corpus, where we already know which dbSNP entry is associated with this gene.

Methods in de.hu.berlin.wbi.objects that return types with arguments of type MutationMention

Modifier and Type	Method and Description
static Map<Integer,List<MutationMention>>	MutationMention.readMutations(String file) This method loads Mutations from a file which are in the following format described in data/snps.txt (PMID\tWMutM\tstart\tstop)

Uses of MutationMention in seth

Methods in seth that return types with arguments of type MutationMention

Modifier and Type	Method and Description
List<MutationMention>	dbSNPRecognizer.extractMutations(String text) FInd dbSNP mentions in a text
List<MutationMention>	OldNomenclature.extractMutations(String text) Extracts mentions of mutations from natural language text written in deprecated nomenclature
List<MutationMention>	SETH.findMutations(String text) Searches for mutation mentions in applied text and returns them

Uses of MutationMention in seth.ner.wrapper

Methods in seth.ner.wrapper that return types with arguments of type MutationMention

Modifier and Type	Method and Description
List<MutationMention>	SETHNER.extractMutations(String text) Extracts mentions of mutations written in the HGVS nomenclature from natural language text