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

Class ProteinVariant

java.lang.Object

de.charite.compbio.jannovar.hgvs.HGVSVariant

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

All Implemented Interfaces:

ConvertibleToHGVSString

Direct Known Subclasses:

MultiAlleleProteinVariant, SingleAlleleProteinVariant

public abstract class ProteinVariant
extends HGVSVariant

Base class for protein changes.

Author:

Manuel Holtgrewe

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_PROTEIN_ISOFORM

Constructor Summary

Constructors

Constructor and Description
ProteinVariant(String refID) Set variant's reference ID, protein ID is null, isoform is NO_PROTEIN_ISOFORM.
ProteinVariant(String refID, String proteinID, int proteinIsoform) Set variant's reference ID, protein ID, and protein isoform to the given value

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
String	getProteinID()
String	getSequenceNamePrefix()
int	hashCode()
String	toHGVSString() Return HGVS representation in three-letter amino acid code.
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString

toHGVSString

Field Detail

NO_PROTEIN_ISOFORM

public static final int NO_PROTEIN_ISOFORM

See Also:

Constant Field Values

Constructor Detail

ProteinVariant

public ProteinVariant(String refID)

Set variant's reference ID, protein ID is null, isoform is NO_PROTEIN_ISOFORM.

ProteinVariant

public ProteinVariant(String refID,
                      String proteinID,
                      int proteinIsoform)

Set variant's reference ID, protein ID, and protein isoform to the given value

Method Detail

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

getProteinID

public String getProteinID()

Returns:

the protein ID

getSequenceNamePrefix

public String getSequenceNamePrefix()

Returns:

sequence name prefix, e.g. "NM_000109.3(DMD_v2)", or "NM_000109.3".

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object