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

Class NucleotideInversion

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideInversion
extends NucleotideChange

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static NucleotideInversion	build(boolean onlyPredicted, int firstPos, int lastPos, NucleotideSeqDescription seq)
static NucleotideInversion	buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int seqLen)
static NucleotideInversion	buildWithOffset(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, NucleotideSeqDescription seq)
static NucleotideInversion	buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, int seqLen)
static NucleotideInversion	buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset)
static NucleotideInversion	buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstPosOffset, int lastPos, int lastPosOffset, String nts)
static NucleotideInversion	buildWithoutSeqDescription(boolean onlyPredicted, int firstPos, int lastPos)
static NucleotideInversion	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()
NucleotideInversion	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

NucleotideInversion

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

Method Detail

buildWithOffset

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

buildWithOffsetWithSequence

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

buildWithOffsetWithLength

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

buildWithOffsetWithoutSeqDescription

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

build

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

buildWithSequence

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

buildWithLength

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

buildWithoutSeqDescription

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

withOnlyPredicted

public NucleotideInversion 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