de.hu.berlin.wbi.objects

Class TranscriptNormalized

java.lang.Object

de.hu.berlin.wbi.objects.Transcript

de.hu.berlin.wbi.objects.TranscriptNormalized

All Implemented Interfaces:

Comparable<TranscriptNormalized>

public class TranscriptNormalized
extends Transcript
implements Comparable<TranscriptNormalized>

Represents a MutationMention mention which has been successfully normalized to a Transcript .

Author:

Philippe Thomas

Field Summary

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

CDC_sequence, ensg, ensp, enst, entrez, protein_sequence, uniprot

Method Summary

Modifier and Type	Method and Description
int	compareTo(TranscriptNormalized that)
int	getConfidence()
UniprotFeature	getFeature()
EnumSet<MatchOptions>	getMatchType()
boolean	isExactMatch()
boolean	isFeatureMatch()
boolean	isPsm()

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

equals, getCDC_sequence, getEnsg, getEnsp, getEnst, getEntrez, getProtein_sequence, getTranscripts, getUniprot, hashCode, init, toString

Methods inherited from class java.lang.Object

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

Method Detail

getMatchType

public EnumSet<MatchOptions> getMatchType()

isFeatureMatch

public boolean isFeatureMatch()

getFeature

public UniprotFeature getFeature()

compareTo

public int compareTo(TranscriptNormalized that)

Specified by:

compareTo in interface Comparable<TranscriptNormalized>

getConfidence

public int getConfidence()

Returns:

confidence for Normalization

isPsm

public boolean isPsm()

Returns:

true if snp is a protein sequence mutation

isExactMatch

public boolean isExactMatch()

Returns:

true if the normalization required no heuristics