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

Class ProteinFrameshift

java.lang.Object

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

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

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinFrameshift
extends ProteinChange

Protein frame shift change.

Author:

Manuel Holtgrewe

Field Summary

Fields

Modifier and Type	Field	Description
static int	LEN_NO_TER	no terminal is encountered
static int	LEN_SHORT	short change description

Constructor Summary

Constructors

Constructor	Description
ProteinFrameshift(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shiftLength)	Construct ProteinFrameshift with the given values

Method Summary

Modifier and Type	Method	Description
static ProteinFrameshift	build(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shiftLength)	Build new ProteinFrameshift with full settings
static ProteinFrameshift	build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength)	Build new ProteinFrameshift with full settings
static ProteinFrameshift	buildShort(boolean onlyPredicted, ProteinPointLocation position)	Build new ProteinFrameshift short description
static ProteinFrameshift	buildShort(boolean onlyPredicted, String wtAA, int position)	Build new ProteinFrameshift short description
static ProteinFrameshift	buildWithoutTerminal(boolean onlyPredicted, ProteinPointLocation position, String targetAA)	Build new ProteinFrameshift for the case that there is no terminal
static ProteinFrameshift	buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA)	Build new ProteinFrameshift for the case that there is no terminal
boolean	equals(Object obj)
ProteinPointLocation	getPosition()
int	getShiftLength()
String	getTargetAA()
int	hashCode()
boolean	isNoTerminalFrameshfit()
boolean	isShort()
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

Field Detail

LEN_NO_TER

public static final int LEN_NO_TER

no terminal is encountered

See Also:

Constant Field Values

LEN_SHORT

public static final int LEN_SHORT

short change description

See Also:

Constant Field Values

Constructor Detail

ProteinFrameshift

public ProteinFrameshift(boolean onlyPredicted,
                         ProteinPointLocation position,
                         String targetAA,
                         int shiftLength)

Construct ProteinFrameshift with the given values

Method Detail

build

public static ProteinFrameshift build(boolean onlyPredicted,
                                      String wtAA,
                                      int position,
                                      String targetAA,
                                      int shiftLength)

Build new ProteinFrameshift with full settings

build

public static ProteinFrameshift build(boolean onlyPredicted,
                                      ProteinPointLocation position,
                                      String targetAA,
                                      int shiftLength)

Build new ProteinFrameshift with full settings

buildShort

public static ProteinFrameshift buildShort(boolean onlyPredicted,
                                           String wtAA,
                                           int position)

Build new ProteinFrameshift short description

buildShort

public static ProteinFrameshift buildShort(boolean onlyPredicted,
                                           ProteinPointLocation position)

Build new ProteinFrameshift short description

buildWithoutTerminal

public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted,
                                                     String wtAA,
                                                     int position,
                                                     String targetAA)

Build new ProteinFrameshift for the case that there is no terminal

buildWithoutTerminal

public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted,
                                                     ProteinPointLocation position,
                                                     String targetAA)

Build new ProteinFrameshift for the case that there is no terminal

isShort

public boolean isShort()

Returns:

true if this object is a short description of a frame shift.

isNoTerminalFrameshfit

public boolean isNoTerminalFrameshfit()

Returns:

true if this object describes a frameshift without a terminal at the end

getPosition

public ProteinPointLocation getPosition()

Returns:

position of first affected amino acid

getTargetAA

public String getTargetAA()

Returns:

amino acid at position after mutation or null if this is a short description

getShiftLength

public int getShiftLength()

Returns:

shift length, or <= 0 in the case of no terminal symbol (0) or short description (-1)

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