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

Class NucleotideInsertion

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideInsertion
extends NucleotideChange

Insertion into a Nucleotide sequence.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideInsertion(boolean onlyPredicted, NucleotideRange position, NucleotideSeqDescription seq)

Method Summary

Modifier and Type	Method	Description
static NucleotideInsertion	buildWithLength(boolean onlyPredicted, int firstPos, int lastPos)	Build without offset and no sequence description
static NucleotideInsertion	buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int insertedLength)	Build without offset and with length information
static NucleotideInsertion	buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, int insertedLength)	Build with length information
static NucleotideInsertion	buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset)	Build without any sequence description
static NucleotideInsertion	buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, String seq)	Build with sequence
static NucleotideInsertion	buildWithSequence(boolean onlyPredicted, int firstPos, int lastPos, String seq)	Build without offset and with sequence
boolean	equals(Object obj)
NucleotideRange	getRange()
NucleotideSeqDescription	getSeq()
int	hashCode()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toString()
NucleotideInsertion	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

NucleotideInsertion

public NucleotideInsertion(boolean onlyPredicted,
                           NucleotideRange position,
                           NucleotideSeqDescription seq)

Parameters:

onlyPredicted - whether the change was only predicted

position - range of length one giving the insertion position

seq - description of the inserted sequence

Method Detail

buildWithOffsetWithoutSeqDescription

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

Build without any sequence description

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

firstOffset - offset for begin position of insertion

lastPos - end position of insertion

lastOffset - offset for end position of insertion

Returns:

Resulting NucleotideInsertion

buildWithOffsetWithLength

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

Build with length information

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

firstOffset - offset for begin position of insertion

lastPos - end position of insertion

lastOffset - offset for end position of insertion

insertedLength - the number of inserted bases

Returns:

Resulting NucleotideInsertion

buildWithOffsetWithSequence

public static NucleotideInsertion buildWithOffsetWithSequence(boolean onlyPredicted,
                                                              int firstPos,
                                                              int firstOffset,
                                                              int lastPos,
                                                              int lastOffset,
                                                              String seq)

Build with sequence

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

firstOffset - offset for begin position of insertion

lastPos - end position of insertion

lastOffset - offset for end position of insertion

seq - the inserted sequence

Returns:

Resulting NucleotideInsertion

buildWithLength

public static NucleotideInsertion buildWithLength(boolean onlyPredicted,
                                                  int firstPos,
                                                  int lastPos)

Build without offset and no sequence description

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

lastPos - end position of insertion

Returns:

Resulting NucleotideInsertion

buildWithLength

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

Build without offset and with length information

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

lastPos - end position of insertion

insertedLength - the number of inserted bases

Returns:

Resulting NucleotideInsertion

buildWithSequence

public static NucleotideInsertion buildWithSequence(boolean onlyPredicted,
                                                    int firstPos,
                                                    int lastPos,
                                                    String seq)

Build without offset and with sequence

Parameters:

onlyPredicted - whether or not to add marker for "only predicted"

firstPos - begin position of insertion

lastPos - end position of insertion

seq - the inserted sequence

Returns:

Resulting NucleotideInsertion

getRange

public NucleotideRange getRange()

Returns:

range of length 1 with the two bases between which the sequence is inserted

getSeq

public NucleotideSeqDescription getSeq()

Returns:

inserted sequenced

withOnlyPredicted

public NucleotideInsertion 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

hashCode

public int hashCode()

Overrides:

hashCode in class NucleotideChange

equals

public boolean equals(Object obj)

Overrides:

equals in class NucleotideChange