de.hu.berlin.wbi.objects

Class MutationValidation

java.lang.Object

de.hu.berlin.wbi.objects.MutationMention

de.hu.berlin.wbi.objects.MutationValidation

public class MutationValidation
extends MutationMention

This object represents a MutationMention from the validation corpus, where we already know which dbSNP entry is associated with this gene. Therefore this class can be used to evaluate precision, recall and F1 for any normalization method.

Author:

Philippe Thomas

Nested Class Summary

Nested classes/interfaces inherited from class de.hu.berlin.wbi.objects.MutationMention

MutationMention.Tool

Field Summary

Fields inherited from class de.hu.berlin.wbi.objects.MutationMention

ambiguous, location, mutResidue, normalized, nsm, patternId, position, psm, ref, text, tool, transcripts, type, wtResidue

Constructor Summary

Constructors

Constructor and Description
MutationValidation(int dbSNP, EntityOffset location, String wtResidue, String mutResidue, String position, String mutationType, String entity) Constructor

Method Summary

Modifier and Type	Method and Description
int	getDbSNP() Gets the associated dbSNP entry.
String	getEntity() Gets the actual entity mention
String	getMutationType() Gets the either NSM or PSM.
static Map<Integer,List<MutationValidation>>	readMutationsValidation(String file) Reads the mutation from the annotated corpus and returns these mutations.
String	toString() (non-Javadoc)

Methods inherited from class de.hu.berlin.wbi.objects.MutationMention

equals, getBestNormalized, getEnd, getLocation, getMutResidue, getNormalized, getPatternId, getPosition, getRef, getStart, getText, getTool, getTranscripts, getType, getWtResidue, hashCode, isAmbiguous, isNsm, isPsm, normalizeSequences, normalizeSNP, normalizeSNP, readMutations, setAmbiguous, setMutResidue, setNsm, setPatternId, setPosition, setPsm, setWtResidue, toHGVS, toNormalized

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MutationValidation

public MutationValidation(int dbSNP,
                          EntityOffset location,
                          String wtResidue,
                          String mutResidue,
                          String position,
                          String mutationType,
                          String entity)

Constructor

Parameters:

dbSNP - -- Goldstandard dbSNP-IdW

location - -- Location in the text

wtResidue - -- Wildtype Allele (e.g. R)

mutResidue - -- Mutated Allele (e.g. C)

position - -- Mutation mocation (e.g. 271)

Method Detail

getDbSNP

public int getDbSNP()

Gets the associated dbSNP entry.

Returns:

the associated dbSNP entry

getMutationType

public String getMutationType()

Gets the either NSM or PSM.

Returns:

the either NSM or PSM

getEntity

public String getEntity()

Gets the actual entity mention

Returns:

tagged string

readMutationsValidation

public static Map<Integer,List<MutationValidation>> readMutationsValidation(String file)
                                                                     throws IOException

Reads the mutation from the annotated corpus and returns these mutations.

Parameters:

file - Annotated corpus

Returns:

list of correct mutations

Throws:

IOException

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class MutationMention

See Also:

MutationMention.toString()