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

Class ProteinShortSequenceRepeatVariability

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinShortSequenceRepeatVariability
extends ProteinChange

Describes short sequence repeat (SSR) variability.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinShortSequenceRepeatVariability(boolean onlyPredicted, ProteinRange range, int minCount, int maxCount)	Construct with the given values

Method Summary

Modifier and Type	Method	Description
static ProteinShortSequenceRepeatVariability	build(boolean onlyPredicted, ProteinRange range, int minCount, int maxCount)	Factory forwards to ProteinShortSequenceRepeatVariability(boolean, ProteinRange, int, int)
static ProteinShortSequenceRepeatVariability	build(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int minCount, int maxCount)	Factory forwards to build(boolean, ProteinRange, int, int)
boolean	equals(Object obj)
int	getMaxCount()
int	getMinCount()
ProteinRange	getRange()
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

ProteinShortSequenceRepeatVariability

public ProteinShortSequenceRepeatVariability(boolean onlyPredicted,
                                             ProteinRange range,
                                             int minCount,
                                             int maxCount)

Construct with the given values

Method Detail

build

public static ProteinShortSequenceRepeatVariability build(boolean onlyPredicted,
                                                          String firstAA,
                                                          int firstPos,
                                                          String lastAA,
                                                          int lastPos,
                                                          int minCount,
                                                          int maxCount)

Factory forwards to build(boolean, ProteinRange, int, int)

build

public static ProteinShortSequenceRepeatVariability build(boolean onlyPredicted,
                                                          ProteinRange range,
                                                          int minCount,
                                                          int maxCount)

Factory forwards to ProteinShortSequenceRepeatVariability(boolean, ProteinRange, int, int)

getRange

public ProteinRange getRange()

Returns:

range of repeat

getMinCount

public int getMinCount()

Returns:

lower bound on count, inclusive

getMaxCount

public int getMaxCount()

Returns:

upper bound on count, inclusive

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