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

Class NucleotideVariant

java.lang.Object

de.charite.compbio.jannovar.hgvs.HGVSVariant

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

All Implemented Interfaces:

ConvertibleToHGVSString

Direct Known Subclasses:

MultiAlleleNucleotideVariant, SingleAlleleNucleotideVariant

public abstract class NucleotideVariant
extends HGVSVariant

Base class for nucleotide changes.

Author:

Manuel Holtgrewe

Field Summary

Fields

Modifier and Type	Field	Description
static int	NO_TRANSCRIPT_VERSION

Constructor Summary

Constructors

Constructor	Description
NucleotideVariant(SequenceType seqType, String refID)	Set variant's reference ID, protein ID is null, version is NO_TRANSCRIPT_VERSION
NucleotideVariant(SequenceType seqType, String refID, String proteinID, int transcriptVersion)	Set variant's reference ID, protein ID, and protein version to the given value

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
String	getProteinID()
String	getRefID()
String	getRefIDWithVersion()
SequenceType	getSeqType()
String	getSequenceNamePrefix()
int	getTranscriptVersion()
int	hashCode()
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given 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_TRANSCRIPT_VERSION

public static final int NO_TRANSCRIPT_VERSION

See Also:

Constant Field Values

Constructor Detail

NucleotideVariant

public NucleotideVariant(SequenceType seqType,
                         String refID)

Set variant's reference ID, protein ID is null, version is NO_TRANSCRIPT_VERSION

NucleotideVariant

public NucleotideVariant(SequenceType seqType,
                         String refID,
                         String proteinID,
                         int transcriptVersion)

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

Method Detail

getSeqType

public SequenceType getSeqType()

Returns:

type of sequence that the change is one

getRefID

public String getRefID()

Returns:

the reference/transcript ID

getTranscriptVersion

public int getTranscriptVersion()

Returns:

transcript version, NO_TRANSCRIPT_VERSION if no version is given

getProteinID

public String getProteinID()

Returns:

protein ID or null if none

getRefIDWithVersion

public String getRefIDWithVersion()

Returns:

the reference/transcript ID with version, if set

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

getSequenceNamePrefix

public String getSequenceNamePrefix()

Returns:

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