de.charite.compbio.jannovar.hgvs.nts.variant

Class MultiAlleleNucleotideVariant

java.lang.Object

de.charite.compbio.jannovar.hgvs.HGVSVariant

de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

All Implemented Interfaces:

ConvertibleToHGVSString

public class MultiAlleleNucleotideVariant
extends NucleotideVariant

Nucleotide variant having multiple alleles.

Author:

Manuel Holtgrewe

Field Summary

Fields inherited from class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

NO_TRANSCRIPT_VERSION

Constructor Summary

Constructors

Constructor and Description
MultiAlleleNucleotideVariant(SequenceType seqType, String seqID, Collection<NucleotideChangeAllele> alleles) Construct with the given SequenceType, reference/transcript ID and collection of NucleotideChangeAlleles.
MultiAlleleNucleotideVariant(SequenceType seqType, String refID, String proteinID, int transcriptVersion, Collection<NucleotideChangeAllele> alleles) Construct with the given SequenceType, reference/transcript ID, protein ID, transcript version, and collection of NucleotideChangeAlleles.

Method Summary

Modifier and Type	Method and Description
static MultiAlleleNucleotideVariant	build(SequenceType seqType, String seqID, NucleotideChangeAllele... alleles)
boolean	equals(Object obj)
com.google.common.collect.ImmutableList<NucleotideChangeAllele>	getAlleles()
int	hashCode()
String	toHGVSString() Return HGVS representation in three-letter amino acid code.
String	toString()

Methods inherited from class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getProteinID, getRefID, getRefIDWithVersion, getSeqType, getSequenceNamePrefix, getTranscriptVersion, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MultiAlleleNucleotideVariant

public MultiAlleleNucleotideVariant(SequenceType seqType,
                                    String refID,
                                    String proteinID,
                                    int transcriptVersion,
                                    Collection<NucleotideChangeAllele> alleles)

Construct with the given SequenceType, reference/transcript ID, protein ID, transcript version, and collection of NucleotideChangeAlleles.

MultiAlleleNucleotideVariant

public MultiAlleleNucleotideVariant(SequenceType seqType,
                                    String seqID,
                                    Collection<NucleotideChangeAllele> alleles)

Construct with the given SequenceType, reference/transcript ID and collection of NucleotideChangeAlleles.

Method Detail

build

public static MultiAlleleNucleotideVariant build(SequenceType seqType,
                                                 String seqID,
                                                 NucleotideChangeAllele... alleles)

Returns:

single-allele nucleotide variant for the given changes

getAlleles

public com.google.common.collect.ImmutableList<NucleotideChangeAllele> getAlleles()

Returns:

the alleles

toHGVSString

public String toHGVSString()

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toString

public String toString()

Overrides:

toString in class NucleotideVariant

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideVariant

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideVariant