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

Class NucleotideMiscChange

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideMiscChange
extends NucleotideChange

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

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideMiscChange(boolean onlyPredicted, NucleotideMiscChangeType changeType)	Construct with given changeType and onlyPredicted flag.

Method Summary

Modifier and Type	Method	Description
static NucleotideMiscChange	build(boolean onlyPredicted, NucleotideMiscChangeType changeType)	Static factory function that forwards to NucleotideMiscChange(boolean, NucleotideMiscChangeType).
static NucleotideMiscChange	buildFromString(String str)	Build from input string.
boolean	equals(Object obj)
NucleotideMiscChangeType	getChangeType()
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
NucleotideMiscChange	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, toString, wait, wait, wait

Constructor Detail

NucleotideMiscChange

public NucleotideMiscChange(boolean onlyPredicted,
                            NucleotideMiscChangeType 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 NucleotideMiscChange build(boolean onlyPredicted,
                                         NucleotideMiscChangeType changeType)

Static factory function that forwards to NucleotideMiscChange(boolean, NucleotideMiscChangeType).

Parameters:

onlyPredicted - whether or not to set "only predicted" flag

changeType - the NucleotideMiscChangeType to build for

Returns:

resulting NucleotideMiscChange

buildFromString

public static NucleotideMiscChange buildFromString(String str)

Build from input string.

Parameters:

str - String to build from

Returns:

resulting NucleotideMiscChange

withOnlyPredicted

public NucleotideMiscChange withOnlyPredicted(boolean flag)

Specified by:

withOnlyPredicted in class NucleotideChange

Returns:

NucleotideChange with given onlyPredicted value.

getChangeType

public NucleotideMiscChangeType getChangeType()

Returns:

type of this NucleotideMiscChangeType

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

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideChange

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideChange