de.charite.compbio.jannovar.hgvs.protein.variant

Class SingleAlleleProteinVariant

java.lang.Object

de.charite.compbio.jannovar.hgvs.HGVSVariant

de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

All Implemented Interfaces:

ConvertibleToHGVSString

public class SingleAlleleProteinVariant
extends ProteinVariant

Protein change with one allele only.

Author:

Manuel Holtgrewe

Field Summary

Fields inherited from class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

NO_PROTEIN_ISOFORM

Constructor Summary

Constructors

Constructor and Description
SingleAlleleProteinVariant(String proteinID, VariantConfiguration varConfig, Collection<? extends ProteinChange> changes) Construct SingleAlleleProteinVariant

Method Summary

Modifier and Type	Method and Description
static SingleAlleleProteinVariant	build(String proteinID, VariantConfiguration varConfig, ProteinChange... changes)
boolean	equals(Object obj)
ProteinChangeAllele	getAllele()
ProteinChange	getChange()
int	hashCode()
boolean	hasOnlyOneChange()
static SingleAlleleProteinVariant	makeSingleChangeVariant(String proteinID, ProteinChange change)
String	toHGVSString(AminoAcidCode code) Return HGVS representation using the given amino acid code.
String	toString()

Methods inherited from class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

getProteinID, getSequenceNamePrefix, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SingleAlleleProteinVariant

public SingleAlleleProteinVariant(String proteinID,
                                  VariantConfiguration varConfig,
                                  Collection<? extends ProteinChange> changes)

Construct SingleAlleleProteinVariant

Parameters:

proteinID - ID of the protein that the change is on

varConfig - VariantConfiguration of the ProteinChanges in the allele

changes - ProteinChanges to use for the single allele

Method Detail

makeSingleChangeVariant

public static SingleAlleleProteinVariant makeSingleChangeVariant(String proteinID,
                                                                 ProteinChange change)

Returns:

protein variant for one change only

build

public static SingleAlleleProteinVariant build(String proteinID,
                                               VariantConfiguration varConfig,
                                               ProteinChange... changes)

Returns:

single-change SingleAlleleProteinVariant with the given protein ID and VariantConfiguration

hasOnlyOneChange

public boolean hasOnlyOneChange()

Returns:

true if the variant has only one ProteinChange.

getChange

public ProteinChange getChange()

Returns:

first change, convenience method for single-change variants

getAllele

public ProteinChangeAllele getAllele()

Returns:

list of changes

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Parameters:

code - AminoAcidCode to use

Returns:

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

toString

public String toString()

Overrides:

toString in class ProteinVariant

hashCode

public int hashCode()

Overrides:

hashCode in class ProteinVariant

equals

public boolean equals(Object obj)

Overrides:

equals in class ProteinVariant