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

Class NucleotideDeletion

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideDeletion
extends NucleotideChange

Deletion in a nucleotide sequence.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideDeletion(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription seq)

Method Summary

Modifier and Type	Method	Description
static NucleotideDeletion	build(boolean onlyPredicted, int firstPos, int lastPos, NucleotideSeqDescription seq)
static NucleotideDeletion	buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int seqLen)
static NucleotideDeletion	buildWithOffset(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, NucleotideSeqDescription seq)
static NucleotideDeletion	buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, int seqLen)
static NucleotideDeletion	buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset)
static NucleotideDeletion	buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, String nts)
static NucleotideDeletion	buildWithoutSeqDescription(boolean onlyPredicted, int firstPos, int lastPos)
static NucleotideDeletion	buildWithSequence(boolean onlyPredicted, int firstPos, int lastPos, String nts)
boolean	equals(Object obj)
NucleotideRange	getRange()
NucleotideSeqDescription	getSeq()
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toString()
NucleotideDeletion	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

Constructor Detail

NucleotideDeletion

public NucleotideDeletion(boolean onlyPredicted,
                          NucleotideRange range,
                          NucleotideSeqDescription seq)

Method Detail

buildWithOffset

public static NucleotideDeletion buildWithOffset(boolean onlyPredicted,
                                                 int firstPos,
                                                 int firstPosOffset,
                                                 int lastPos,
                                                 int lastPosOffset,
                                                 NucleotideSeqDescription seq)

buildWithOffsetWithSequence

public static NucleotideDeletion buildWithOffsetWithSequence(boolean onlyPredicted,
                                                             int firstPos,
                                                             int firstPosOffset,
                                                             int lastPos,
                                                             int lastPosOffset,
                                                             String nts)

buildWithOffsetWithLength

public static NucleotideDeletion buildWithOffsetWithLength(boolean onlyPredicted,
                                                           int firstPos,
                                                           int firstPosOffset,
                                                           int lastPos,
                                                           int lastPosOffset,
                                                           int seqLen)

buildWithOffsetWithoutSeqDescription

public static NucleotideDeletion buildWithOffsetWithoutSeqDescription(boolean onlyPredicted,
                                                                      int firstPos,
                                                                      int firstPosOffset,
                                                                      int lastPos,
                                                                      int lastPosOffset)

build

public static NucleotideDeletion build(boolean onlyPredicted,
                                       int firstPos,
                                       int lastPos,
                                       NucleotideSeqDescription seq)

buildWithSequence

public static NucleotideDeletion buildWithSequence(boolean onlyPredicted,
                                                   int firstPos,
                                                   int lastPos,
                                                   String nts)

buildWithLength

public static NucleotideDeletion buildWithLength(boolean onlyPredicted,
                                                 int firstPos,
                                                 int lastPos,
                                                 int seqLen)

buildWithoutSeqDescription

public static NucleotideDeletion buildWithoutSeqDescription(boolean onlyPredicted,
                                                            int firstPos,
                                                            int lastPos)

withOnlyPredicted

public NucleotideDeletion withOnlyPredicted(boolean flag)

Specified by:

withOnlyPredicted in class NucleotideChange

Returns:

NucleotideChange with given onlyPredicted value.

getRange

public NucleotideRange getRange()

getSeq

public NucleotideSeqDescription getSeq()

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