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

Class NucleotideUnchanged

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideUnchanged
extends NucleotideChange

Unchanged in a nucleotide sequence.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

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

Method Summary

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

NucleotideUnchanged

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

Method Detail

buildWithOffset

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

buildWithOffsetWithSequence

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

buildWithOffsetWithLength

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

buildWithOffsetWithoutSeqDescription

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

build

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

buildWithSequence

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

buildWithLength

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

buildWithoutSeqDescription

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

withOnlyPredicted

public NucleotideUnchanged 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