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

Class NucleotideSequencedRepeat

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideSequencedRepeat
extends NucleotideChange

A repeat that has been sequenced.

Author:

Mark Woon

Field Summary

Fields

Modifier and Type	Field	Description
NucleotideNotSequencedRepeat	notSequencedRepeat
List<NucleotideRepeatSequence>	sequencedRepeats

Constructor Summary

Constructors

Constructor	Description
NucleotideSequencedRepeat(boolean onlyPredicted, NucleotideRange range, List<NucleotideRepeatSequence> sequencedRepeats)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
NucleotideNotSequencedRepeat	getNotSequencedRepeat()	Gets the repeat if it was not sequenced.
NucleotideRange	getRange()
List<NucleotideRepeatSequence>	getSequencedRepeats()	Gets the sequenced repeats.
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toString()
NucleotideChange	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

Field Detail

sequencedRepeats

public List<NucleotideRepeatSequence> sequencedRepeats

notSequencedRepeat

public NucleotideNotSequencedRepeat notSequencedRepeat

Constructor Detail

NucleotideSequencedRepeat

public NucleotideSequencedRepeat(boolean onlyPredicted,
                                 NucleotideRange range,
                                 List<NucleotideRepeatSequence> sequencedRepeats)

Method Detail

getRange

public NucleotideRange getRange()

Returns:

range of repeat

getSequencedRepeats

public List<NucleotideRepeatSequence> getSequencedRepeats()

Gets the sequenced repeats. Null if this repeat is not sequenced.

getNotSequencedRepeat

public NucleotideNotSequencedRepeat getNotSequencedRepeat()

Gets the repeat if it was not sequenced. Null if this repeat is sequenced.

withOnlyPredicted

public NucleotideChange withOnlyPredicted(boolean flag)

Specified by:

withOnlyPredicted in class NucleotideChange

Returns:

NucleotideChange with given onlyPredicted value.

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