de.hu.berlin.wbi.objects

Class dbSNPNormalized

java.lang.Object

de.hu.berlin.wbi.objects.dbSNP

de.hu.berlin.wbi.objects.dbSNPNormalized

All Implemented Interfaces:

Comparable<dbSNPNormalized>

public class dbSNPNormalized
extends dbSNP
implements Comparable<dbSNPNormalized>

Represents a MutationMention mention which has been successfully normalized to a dbSNP . Therefore it extends dbSNP.

Author:

Philippe Thomas

Field Summary

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

aaPosition, geneID, hgvs, residues, rsID, wildtype

Constructor Summary

Constructors

Constructor and Description
dbSNPNormalized(dbSNP dbsnp, EnumSet<MatchOptions> matchType, UniprotFeature feature)

Method Summary

Modifier and Type	Method and Description
int	compareTo(dbSNPNormalized that)
int	getConfidence()
UniprotFeature	getFeature()
EnumSet<MatchOptions>	getMatchType()
boolean	isAlleleOrder() Returns true if Alleles are in the same order in dbSNP as in the text mention
boolean	isExactPosition()
boolean	isFeatureMatch()
boolean	isMethioneMatch()
boolean	isPsm()
String	toString() (non-Javadoc)

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

equals, getAaPosition, getGeneID, getHgvs, getResidues, getRsID, getSNP, getWildtype, hashCode, init, setAaPosition, setGeneID, setHgvs, setResidues, setRsID

Methods inherited from class java.lang.Object

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

Constructor Detail

dbSNPNormalized

public dbSNPNormalized(dbSNP dbsnp,
                       EnumSet<MatchOptions> matchType,
                       UniprotFeature feature)

Parameters:

dbsnp - dbSNP Object

feature - UniProt feature used for normalization

matchType - EnumSet of MatchOptions enum values

Method Detail

getMatchType

public EnumSet<MatchOptions> getMatchType()

getConfidence

public int getConfidence()

Returns:

confidence for Normalization

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class dbSNP

See Also:

dbSNP.toString()

isAlleleOrder

public boolean isAlleleOrder()

Returns true if Alleles are in the same order in dbSNP as in the text mention

isExactPosition

public boolean isExactPosition()

Returns:

true if the location of the mutation is exact

isMethioneMatch

public boolean isMethioneMatch()

Returns:

true if position has an offset of +/-1 but otherwise there's a match

isFeatureMatch

public boolean isFeatureMatch()

getFeature

public UniprotFeature getFeature()

isPsm

public boolean isPsm()

Returns:

true if snp is a protein sequence mutation

compareTo

public int compareTo(dbSNPNormalized that)

Specified by:

compareTo in interface Comparable<dbSNPNormalized>