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

Class ProteinDuplication

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinDuplication
extends ProteinChange

Constructor Summary

Constructors

Constructor and Description
ProteinDuplication(boolean onlyPredicted, ProteinRange range, ProteinSeqDescription seqSpec)

Method Summary

Modifier and Type	Method and Description
static ProteinDuplication	buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int len)
static ProteinDuplication	buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
static ProteinDuplication	buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription desc)
static ProteinDuplication	buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)
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

ProteinDuplication

public ProteinDuplication(boolean onlyPredicted,
                          ProteinRange range,
                          ProteinSeqDescription seqSpec)

Parameters:

onlyPredicted -

range -

seqSpec -

Method Detail

buildWithoutSeqDescription

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

buildWithSequence

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

buildWithLength

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

buildWithSeqDescription

public static ProteinDuplication buildWithSeqDescription(boolean onlyPredicted,
                                                         String firstAA,
                                                         int firstPos,
                                                         String lastAA,
                                                         int lastPos,
                                                         ProteinSeqDescription desc)

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