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

Class NucleotideIndel

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideIndel
extends NucleotideChange

Constructor Summary

Constructors

Constructor	Description
NucleotideIndel(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription delSeq, NucleotideSeqDescription insSeq)

Method Summary

Modifier and Type	Method	Description
static NucleotideIndel	buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int deletedLength, int insertedLength)	Build without offset and with length information
static NucleotideIndel	buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, int deletedLength, int insertedLength)	Build with length information
static NucleotideIndel	buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset)	Build without any sequence description
static NucleotideIndel	buildWithOffsetWithSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, NucleotideSeqDescription delDesc, NucleotideSeqDescription insDesc)	Build with sequence description
static NucleotideIndel	buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, String deletedSeq, String insertedSeq)	Build with sequence information
static NucleotideIndel	buildWithoutSeqDescription(boolean onlyPredicted, int firstPos, int lastPos)	Build without offset and any sequence description
static NucleotideIndel	buildWithSeqDescription(boolean onlyPredicted, int firstPos, int lastPos, NucleotideSeqDescription delDesc, NucleotideSeqDescription insDesc)	Build without offset and with sequence description
static NucleotideIndel	buildWithSequence(boolean onlyPredicted, int firstPos, int lastPos, String deletedSeq, String insertedSeq)	Build without offset and with sequence information
boolean	equals(Object obj)
NucleotideSeqDescription	getDelSeq()
NucleotideSeqDescription	getInsSeq()
NucleotideRange	getRange()
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toString()
NucleotideIndel	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

NucleotideIndel

public NucleotideIndel(boolean onlyPredicted,
                       NucleotideRange range,
                       NucleotideSeqDescription delSeq,
                       NucleotideSeqDescription insSeq)

Method Detail

buildWithOffsetWithoutSeqDescription

public static NucleotideIndel buildWithOffsetWithoutSeqDescription(boolean onlyPredicted,
                                                                   int firstPos,
                                                                   int firstOffset,
                                                                   int lastPos,
                                                                   int lastOffset)

Build without any sequence description

buildWithOffsetWithLength

public static NucleotideIndel buildWithOffsetWithLength(boolean onlyPredicted,
                                                        int firstPos,
                                                        int firstOffset,
                                                        int lastPos,
                                                        int lastOffset,
                                                        int deletedLength,
                                                        int insertedLength)

Build with length information

buildWithOffsetWithSequence

public static NucleotideIndel buildWithOffsetWithSequence(boolean onlyPredicted,
                                                          int firstPos,
                                                          int firstOffset,
                                                          int lastPos,
                                                          int lastOffset,
                                                          String deletedSeq,
                                                          String insertedSeq)

Build with sequence information

buildWithOffsetWithSeqDescription

public static NucleotideIndel buildWithOffsetWithSeqDescription(boolean onlyPredicted,
                                                                int firstPos,
                                                                int firstOffset,
                                                                int lastPos,
                                                                int lastOffset,
                                                                NucleotideSeqDescription delDesc,
                                                                NucleotideSeqDescription insDesc)

Build with sequence description

buildWithoutSeqDescription

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

Build without offset and any sequence description

buildWithLength

public static NucleotideIndel buildWithLength(boolean onlyPredicted,
                                              int firstPos,
                                              int lastPos,
                                              int deletedLength,
                                              int insertedLength)

Build without offset and with length information

buildWithSequence

public static NucleotideIndel buildWithSequence(boolean onlyPredicted,
                                                int firstPos,
                                                int lastPos,
                                                String deletedSeq,
                                                String insertedSeq)

Build without offset and with sequence information

buildWithSeqDescription

public static NucleotideIndel buildWithSeqDescription(boolean onlyPredicted,
                                                      int firstPos,
                                                      int lastPos,
                                                      NucleotideSeqDescription delDesc,
                                                      NucleotideSeqDescription insDesc)

Build without offset and with sequence description

withOnlyPredicted

public NucleotideIndel 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

getRange

public NucleotideRange getRange()

getInsSeq

public NucleotideSeqDescription getInsSeq()

getDelSeq

public NucleotideSeqDescription getDelSeq()

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideChange

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideChange