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

Class NucleotideRange

java.lang.Object

de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideRange
extends Object
implements ConvertibleToHGVSString

Range in a nucleotide sequence.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideRange(NucleotidePointLocation firstPos, NucleotidePointLocation lastPost)

Method Summary

Modifier and Type	Method	Description
static NucleotideRange	build(int firstPos, int firstPosOffset, int lastPos, int lastPosOffset)
static NucleotideRange	buildWithoutOffset(int firstPos, int lastPos)
boolean	equals(Object obj)
NucleotidePointLocation	getFirstPos()
NucleotidePointLocation	getLastPos()
int	hashCode()
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

NucleotideRange

public NucleotideRange(NucleotidePointLocation firstPos,
                       NucleotidePointLocation lastPost)

Parameters:

firstPos -

lastPost -

Method Detail

build

public static NucleotideRange build(int firstPos,
                                    int firstPosOffset,
                                    int lastPos,
                                    int lastPosOffset)

buildWithoutOffset

public static NucleotideRange buildWithoutOffset(int firstPos,
                                                 int lastPos)

getFirstPos

public NucleotidePointLocation getFirstPos()

getLastPos

public NucleotidePointLocation getLastPos()

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