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

Class NucleotidePointLocation

java.lang.Object

de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotidePointLocation
extends Object
implements ConvertibleToHGVSString

Position in a nucleotide string.

Characterized by a 1-based position in the current coordinate system (e.g. CDS) with an offset into the exon/intron.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotidePointLocation(int basePos)	Deprecated.
NucleotidePointLocation(int basePos, int offset, boolean downstreamOfCDS)	Construct with given base position and offset

Method Summary

Modifier and Type	Method	Description
static NucleotidePointLocation	build(int basePos)
static NucleotidePointLocation	buildDownstreamOfCDS(int basePos)
static NucleotidePointLocation	buildWithOffset(int basePos, int offset)
boolean	equals(Object obj)
int	getBasePos()
int	getOffset()
int	hashCode()
boolean	isDownstreamOfCDS()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
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

Constructor Detail

NucleotidePointLocation

@Deprecated
public NucleotidePointLocation(int basePos)

Deprecated.

Construct with given base position.

Parameters:

basePos - 0-based position in the nucleotide string

NucleotidePointLocation

public NucleotidePointLocation(int basePos,
                               int offset,
                               boolean downstreamOfCDS)

Construct with given base position and offset

Parameters:

basePos - 0-based position in the nucleotide string

offset - 1-based offset (only non-0 values are allowed)

downstreamOfCDS - true if downstream of CDS

Method Detail

build

public static NucleotidePointLocation build(int basePos)

buildWithOffset

public static NucleotidePointLocation buildWithOffset(int basePos,
                                                      int offset)

buildDownstreamOfCDS

public static NucleotidePointLocation buildDownstreamOfCDS(int basePos)

getBasePos

public int getBasePos()

getOffset

public int getOffset()

isDownstreamOfCDS

public boolean isDownstreamOfCDS()

toHGVSString

public String toHGVSString()

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Returns:

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

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Parameters:

code - AminoAcidCode to use

Returns:

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

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