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

Class ProteinDeletion

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinDeletion
extends ProteinChange

In-frame deletion of a protein (i.e., without frameshift, but can destroy codons).

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinDeletion(boolean onlyPredicted, ProteinRange range)	Construct ProteinDeletion without length and sequence information
ProteinDeletion(boolean onlyPredicted, ProteinRange range, int length)	Construct ProteinDeletion with length information
ProteinDeletion(boolean onlyPredicted, ProteinRange range, String seq)	Construct ProteinDeletion with sequence information

Method Summary

Modifier and Type	Method	Description
static ProteinDeletion	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int length)	Construct ProteinDeletion with length information
static ProteinDeletion	buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)	Construct ProteinDeletion without length and sequence information
static ProteinDeletion	buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)	Construct ProteinDeletion with sequence
ProteinRange	getRange()
ProteinSeqDescription	getSeqDesc()
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given amino acid code.
ProteinChange	withOnlyPredicted(boolean onlyPredicted)

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

equals, hashCode, isOnlyPredicted, toHGVSString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProteinDeletion

public ProteinDeletion(boolean onlyPredicted,
                       ProteinRange range)

Construct ProteinDeletion without length and sequence information

ProteinDeletion

public ProteinDeletion(boolean onlyPredicted,
                       ProteinRange range,
                       int length)

Construct ProteinDeletion with length information

ProteinDeletion

public ProteinDeletion(boolean onlyPredicted,
                       ProteinRange range,
                       String seq)

Construct ProteinDeletion with sequence information

Method Detail

buildWithoutSeqDescription

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

Construct ProteinDeletion without length and sequence information

buildWithLength

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

Construct ProteinDeletion with length information

buildWithSequence

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

Construct ProteinDeletion with sequence

getRange

public ProteinRange getRange()

Returns:

deleted range in the protein

getSeqDesc

public ProteinSeqDescription getSeqDesc()

Returns:

description of the deleted sequence

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

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