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

Class SingleAlleleNucleotideVariant

java.lang.Object

de.charite.compbio.jannovar.hgvs.HGVSVariant

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class SingleAlleleNucleotideVariant
extends NucleotideVariant

Nucleotide change with one allele only.

Author:

Manuel Holtgrewe

Field Summary

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

NO_TRANSCRIPT_VERSION

Constructor Summary

Constructors

Constructor	Description
SingleAlleleNucleotideVariant(SequenceType seqType, String seqID, NucleotideChangeAllele allele)	Construct SingleAlleleNucleotideVariant
SingleAlleleNucleotideVariant(SequenceType seqType, String seqID, VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes)	Construct SingleAlleleNucleotideVariant
SingleAlleleNucleotideVariant(SequenceType seqType, String refID, String proteinID, int transcriptVersion, NucleotideChangeAllele allele)	Construct SingleAlleleNucleotideVariant

Method Summary

Modifier and Type	Method	Description
static SingleAlleleNucleotideVariant	build(SequenceType seqType, String seqID, VariantConfiguration varConfig, NucleotideChange... changes)
boolean	equals(Object obj)
NucleotideChangeAllele	getAllele()
NucleotideChange	getChange()
int	hashCode()
boolean	hasOnlyOneChange()
static SingleAlleleNucleotideVariant	makeSingleChangeVariant(SequenceType seqType, String seqID, NucleotideChange change)
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.

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

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SingleAlleleNucleotideVariant

public SingleAlleleNucleotideVariant(SequenceType seqType,
                                     String seqID,
                                     VariantConfiguration varConfig,
                                     Collection<? extends NucleotideChange> changes)

Construct SingleAlleleNucleotideVariant

Parameters:

seqType - type of the changed sequence

seqID - ID of the reference/transcript that the change is on

varConfig - VariantConfiguration of the NucleotideChanges in the allele

changes - NucleotideChanges to use for the single allele

SingleAlleleNucleotideVariant

public SingleAlleleNucleotideVariant(SequenceType seqType,
                                     String refID,
                                     String proteinID,
                                     int transcriptVersion,
                                     NucleotideChangeAllele allele)

Construct SingleAlleleNucleotideVariant

SingleAlleleNucleotideVariant

public SingleAlleleNucleotideVariant(SequenceType seqType,
                                     String seqID,
                                     NucleotideChangeAllele allele)

Construct SingleAlleleNucleotideVariant

Parameters:

seqType - type of the changed sequence

seqID - ID of the reference/transcript that the change is on

allele - NucleotideChangeAllele to use

Method Detail

makeSingleChangeVariant

public static SingleAlleleNucleotideVariant makeSingleChangeVariant(SequenceType seqType,
                                                                    String seqID,
                                                                    NucleotideChange change)

Returns:

nucleotide variant for one change only

build

public static SingleAlleleNucleotideVariant build(SequenceType seqType,
                                                  String seqID,
                                                  VariantConfiguration varConfig,
                                                  NucleotideChange... changes)

Returns:

single-change SingleAlleleNucleotideVariant with the given SequenceType, reference/transcript ID, and VariantConfiguration

hasOnlyOneChange

public boolean hasOnlyOneChange()

Returns:

true if the variant has only one NucleotideChange.

getChange

public NucleotideChange getChange()

Returns:

first change, convenience method for single-change variants

getAllele

public NucleotideChangeAllele getAllele()

Returns:

list of changes

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

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideVariant

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideVariant