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

Class ProteinIndel

java.lang.Object

de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinIndel
extends ProteinChange

In-frame substitution on the protein level with more than one base.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinIndel(boolean onlyPredicted, ProteinRange range, ProteinSeqDescription delSeq, ProteinSeqDescription insSeq)

Method Summary

Modifier and Type	Method	Description
static ProteinIndel	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int deletedLength, int insertedLength)	Build with length information
static ProteinIndel	buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)	Build without any sequence description
static ProteinIndel	buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription delDesc, ProteinSeqDescription insDesc)	Build with sequence description
static ProteinIndel	buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String deletedSeq, String insertedSeq)	Build with sequence information
boolean	equals(Object obj)
ProteinRange	getRange()
ProteinSeqDescription	getSeq()
int	hashCode()
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given amino acid code.
String	toString()
ProteinChange	withOnlyPredicted(boolean onlyPredicted)

Methods inherited from class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

isOnlyPredicted, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ProteinIndel

public ProteinIndel(boolean onlyPredicted,
                    ProteinRange range,
                    ProteinSeqDescription delSeq,
                    ProteinSeqDescription insSeq)

Method Detail

buildWithoutSeqDescription

public static ProteinIndel buildWithoutSeqDescription(boolean onlyPredicted,
                                                      String firstAA,
                                                      int firstPos,
                                                      String lastAA,
                                                      int lastPos)

Build without any sequence description

buildWithLength

public static ProteinIndel buildWithLength(boolean onlyPredicted,
                                           String firstAA,
                                           int firstPos,
                                           String lastAA,
                                           int lastPos,
                                           int deletedLength,
                                           int insertedLength)

Build with length information

buildWithSequence

public static ProteinIndel buildWithSequence(boolean onlyPredicted,
                                             String firstAA,
                                             int firstPos,
                                             String lastAA,
                                             int lastPos,
                                             String deletedSeq,
                                             String insertedSeq)

Build with sequence information

buildWithSeqDescription

public static ProteinIndel buildWithSeqDescription(boolean onlyPredicted,
                                                   String firstAA,
                                                   int firstPos,
                                                   String lastAA,
                                                   int lastPos,
                                                   ProteinSeqDescription delDesc,
                                                   ProteinSeqDescription insDesc)

Build with sequence description

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Parameters:

code - AminoAcidCode to use

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toString

public String toString()

Overrides:

toString in class Object

getRange

public ProteinRange getRange()

getSeq

public ProteinSeqDescription getSeq()

hashCode

public int hashCode()

Overrides:

hashCode in class ProteinChange

equals

public boolean equals(Object obj)

Overrides:

equals in class ProteinChange

withOnlyPredicted

public ProteinChange withOnlyPredicted(boolean onlyPredicted)

Specified by:

withOnlyPredicted in class ProteinChange

Returns:

ProteinChange object with prediction state set to the one given by the parameter