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

Class ProteinPointLocation

java.lang.Object

de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinPointLocation
extends Object
implements ConvertibleToHGVSString

Represent one position in a protein.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinPointLocation(String aa, int pos, int offset, boolean downstreamOfTerminal)

Method Summary

Modifier and Type	Method	Description
static ProteinPointLocation	build(String aa, int pos)
static ProteinPointLocation	buildDownstreamOfTerminal(String aa, int pos)
static ProteinPointLocation	buildWithOffset(String aa, int pos, int offset)
boolean	equals(Object obj)
String	getAA()
int	getOffset()
int	getPos()
int	hashCode()
boolean	isDownstreamOfTerminal()
String	toHGVSString()	Return HGVS representation in three-letter amino acid code.
String	toHGVSString(AminoAcidCode code)	Return HGVS representation using the given amino acid code.
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ProteinPointLocation

public ProteinPointLocation(String aa,
                            int pos,
                            int offset,
                            boolean downstreamOfTerminal)

Parameters:

aa - 1-letter code of the amino acid

pos - 0-based position in the protein

offset - for changes in intronic or upstream regions, 0 for no offset

Method Detail

build

public static ProteinPointLocation build(String aa,
                                         int pos)

buildWithOffset

public static ProteinPointLocation buildWithOffset(String aa,
                                                   int pos,
                                                   int offset)

buildDownstreamOfTerminal

public static ProteinPointLocation buildDownstreamOfTerminal(String aa,
                                                             int pos)

getPos

public int getPos()

Returns:

0-based position in the amino acid

getAA

public String getAA()

Returns:

1-letter code of the amino acid

getOffset

public int getOffset()

Returns:

offset for changes in intronic or upstream regions, 0 for no offset

isDownstreamOfTerminal

public boolean isDownstreamOfTerminal()

Returns:

positions is downstream of the translational terminal codon, e.g. for Gln*1

toHGVSString

public String toHGVSString()

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Returns:

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

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

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 Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object