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

Class NucleotideNotSequencedRepeat

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideNotSequencedRepeat
extends NucleotideChange

A repeat that is not completely sequenced (i.e. unknown bases).

Author:

Mark Woon

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	NucleotideNotSequencedRepeat.InDelType

Constructor Summary

Constructors

Constructor	Description
NucleotideNotSequencedRepeat(boolean onlyPredicted, NucleotideRange range, NucleotideNotSequencedRepeat.InDelType type, int minCount, int maxCount)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
int	getMaxCount()	Gets the upper bound on the length of the repeat, inclusive.
int	getMinCount()	Gets the lower bound on the length of the repeat, inclusive.
NucleotideRange	getRange()
int	hashCode()
boolean	isDeletion()
boolean	isInsertion()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given amino acid code.
String	toString()
NucleotideChange	withOnlyPredicted(boolean flag)

Methods inherited from class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

isOnlyPredicted

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

NucleotideNotSequencedRepeat

public NucleotideNotSequencedRepeat(boolean onlyPredicted,
                                    NucleotideRange range,
                                    NucleotideNotSequencedRepeat.InDelType type,
                                    int minCount,
                                    int maxCount)

Method Detail

getRange

public NucleotideRange getRange()

Returns:

range of repeat

isInsertion

public boolean isInsertion()

isDeletion

public boolean isDeletion()

getMinCount

public int getMinCount()

Gets the lower bound on the length of the repeat, inclusive.

getMaxCount

public int getMaxCount()

Gets the upper bound on the length of the repeat, inclusive.

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

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Overrides:

toHGVSString in class NucleotideChange

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 NucleotideChange

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideChange