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

Class ProteinExtension

java.lang.Object

de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinExtension
extends ProteinChange

Field Summary

Fields

Modifier and Type	Field	Description
static int	LEN_NO_TER	no terminal is encountered

Constructor Summary

Constructors

Constructor	Description
ProteinExtension(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shift)	Construct ProteinExtension with the given values

Method Summary

Modifier and Type	Method	Description
static ProteinExtension	build(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shift)	Construct normal ProteinExtension
static ProteinExtension	build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift)	Construct normal ProteinExtension
static ProteinExtension	buildWithoutTerminal(boolean onlyPredicted, ProteinPointLocation position, String targetAA)	Construct ProteinExtension without a terminal in the extension
static ProteinExtension	buildWithoutTerminal(boolean onlyPredicted, String wtAA, int pos, String targetAA)	Construct ProteinExtension without a terminal in the extension
boolean	equals(Object obj)
ProteinPointLocation	getPosition()
int	getShift()	The shift value number of extended amino acids if positive, shift into the 5' UTR in case of negative values, or LEN_NO_TER in the case that no stop codon is encountered on the transcript.
String	getTargetAA()
int	hashCode()
boolean	isNoTerminalExtension()
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given amino acid code.
String	toString()
ProteinChange	withOnlyPredicted(boolean onlyPredicted)

Methods inherited from class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

isOnlyPredicted, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

LEN_NO_TER

public static final int LEN_NO_TER

no terminal is encountered

See Also:

Constant Field Values

Constructor Detail

ProteinExtension

public ProteinExtension(boolean onlyPredicted,
                        ProteinPointLocation position,
                        String targetAA,
                        int shift)

Construct ProteinExtension with the given values

Method Detail

build

public static ProteinExtension build(boolean onlyPredicted,
                                     String wtAA,
                                     int pos,
                                     String targetAA,
                                     int shift)

Construct normal ProteinExtension

build

public static ProteinExtension build(boolean onlyPredicted,
                                     ProteinPointLocation position,
                                     String targetAA,
                                     int shift)

Construct normal ProteinExtension

buildWithoutTerminal

public static ProteinExtension buildWithoutTerminal(boolean onlyPredicted,
                                                    String wtAA,
                                                    int pos,
                                                    String targetAA)

Construct ProteinExtension without a terminal in the extension

buildWithoutTerminal

public static ProteinExtension buildWithoutTerminal(boolean onlyPredicted,
                                                    ProteinPointLocation position,
                                                    String targetAA)

Construct ProteinExtension without a terminal in the extension

getPosition

public ProteinPointLocation getPosition()

Returns:

changed amino acid and its position

getTargetAA

public String getTargetAA()

Returns:

amino acid that the changed one is changed to

getShift

public int getShift()

The shift value number of extended amino acids if positive, shift into the 5' UTR in case of negative values, or LEN_NO_TER in the case that no stop codon is encountered on the transcript.

Returns:

shift value of the extension

isNoTerminalExtension

public boolean isNoTerminalExtension()

Returns:

true if this object describes an extension without a terminal at the end

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

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class ProteinChange

equals

public boolean equals(Object obj)

Overrides:

equals in class ProteinChange

withOnlyPredicted

public ProteinChange withOnlyPredicted(boolean onlyPredicted)

Specified by:

withOnlyPredicted in class ProteinChange

Returns:

ProteinChange object with prediction state set to the one given by the parameter