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

Class ProteinMiscChange

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinMiscChange
extends ProteinChange

Represents a silent protein-level change, i.e., "p.=".

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinMiscChange(boolean onlyPredicted, ProteinMiscChangeType changeType)	Construct with given changeType and onlyPredicted flag.

Method Summary

Modifier and Type	Method	Description
static ProteinMiscChange	build(boolean onlyPredicted, ProteinMiscChangeType changeType)	Static factory function that forwards to ProteinMiscChange(boolean, ProteinMiscChangeType).
boolean	equals(Object obj)
ProteinMiscChangeType	getChangeType()
int	hashCode()
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

Constructor Detail

ProteinMiscChange

public ProteinMiscChange(boolean onlyPredicted,
                         ProteinMiscChangeType changeType)

Construct with given changeType and onlyPredicted flag.

Parameters:

onlyPredicted - whether or not the change is only predicted

changeType - type of the change

Method Detail

build

public static ProteinMiscChange build(boolean onlyPredicted,
                                      ProteinMiscChangeType changeType)

Static factory function that forwards to ProteinMiscChange(boolean, ProteinMiscChangeType).

getChangeType

public ProteinMiscChangeType getChangeType()

Returns:

type of this ProteinMiscChangeType

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

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

toString

public String toString()

Overrides:

toString in class Object