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

Class ProteinInsertion

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinInsertion
extends ProteinChange

Insertion into a protein sequence.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
ProteinInsertion(boolean onlyPredicted, ProteinRange position, ProteinSeqDescription seq)

Method Summary

Modifier and Type	Method and Description
static ProteinInsertion	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos) Build without any sequence description.
static ProteinInsertion	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int insertedLength) Build with length information
static ProteinInsertion	buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos) Build without any SeqDescription
static ProteinInsertion	buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription seqDescription) Build with SeqDescription
static ProteinInsertion	buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq) Build with sequence
boolean	equals(Object obj)
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

ProteinInsertion

public ProteinInsertion(boolean onlyPredicted,
                        ProteinRange position,
                        ProteinSeqDescription 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

buildWithLength

public static ProteinInsertion buildWithLength(boolean onlyPredicted,
                                               String firstAA,
                                               int firstPos,
                                               String lastAA,
                                               int lastPos)

Build without any sequence description.

buildWithLength

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

Build with length information

buildWithSequence

public static ProteinInsertion buildWithSequence(boolean onlyPredicted,
                                                 String firstAA,
                                                 int firstPos,
                                                 String lastAA,
                                                 int lastPos,
                                                 String seq)

Build with sequence

buildWithSeqDescription

public static ProteinInsertion buildWithSeqDescription(boolean onlyPredicted,
                                                       String firstAA,
                                                       int firstPos,
                                                       String lastAA,
                                                       int lastPos,
                                                       ProteinSeqDescription seqDescription)

Build with SeqDescription

buildWithoutSeqDescription

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

Build without any SeqDescription

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

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