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

Class ProteinUnchanged

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinUnchanged
extends ProteinChange

Unchanged mark inside protein.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static ProteinUnchanged	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int length)	Construct ProteinDeletion with length information
static ProteinUnchanged	buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)	Construct ProteinDeletion without length and sequence information
static ProteinUnchanged	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

ProteinUnchanged

public ProteinUnchanged(boolean onlyPredicted,
                        ProteinRange range)

Construct ProteinDeletion without length and sequence information

ProteinUnchanged

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

Construct ProteinDeletion with length information

ProteinUnchanged

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

Construct ProteinDeletion with sequence information

Method Detail

buildWithoutSeqDescription

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

Construct ProteinDeletion without length and sequence information

buildWithLength

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

Construct ProteinDeletion with length information

buildWithSequence

public static ProteinUnchanged 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