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

Class NucleotideSubstitution

java.lang.Object

de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideSubstitution
extends NucleotideChange

Substitution of one nucleotide.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT)	Construct with the given values

Method Summary

Modifier and Type	Method	Description
static NucleotideSubstitution	build(boolean onlyPredicted, int basePos, String fromNT, String toNT)	Build NucleotideSubstitution with nucleotide positions without offset values.
static NucleotideSubstitution	buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT)	Build NucleotideSubstitution with nucleotide positions with offset values.
boolean	equals(Object obj)
String	getFromNT()
NucleotidePointLocation	getPosition()
String	getToNT()
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toString()
NucleotideSubstitution	withOnlyPredicted(boolean flag)

Methods inherited from class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

isOnlyPredicted, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

NucleotideSubstitution

public NucleotideSubstitution(boolean onlyPredicted,
                              NucleotidePointLocation position,
                              String fromNT,
                              String toNT)

Construct with the given values

Method Detail

buildWithOffset

public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted,
                                                     int basePos,
                                                     int posOffset,
                                                     String fromNT,
                                                     String toNT)

Build NucleotideSubstitution with nucleotide positions with offset values.

build

public static NucleotideSubstitution build(boolean onlyPredicted,
                                           int basePos,
                                           String fromNT,
                                           String toNT)

Build NucleotideSubstitution with nucleotide positions without offset values.

withOnlyPredicted

public NucleotideSubstitution withOnlyPredicted(boolean flag)

Specified by:

withOnlyPredicted in class NucleotideChange

Returns:

NucleotideChange with given onlyPredicted value.

getPosition

public NucleotidePointLocation getPosition()

Returns:

NucleotidePointLocation of the changed nucleotide

getFromNT

public String getFromNT()

Returns:

reference nucleotide

getToNT

public String getToNT()

Returns:

variant nucleotide

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

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideChange

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideChange