public class ProteinExtension extends ProteinChange
Modifier and Type | Field and Description |
---|---|
static int |
LEN_NO_TER
no terminal is encountered
|
Constructor and Description |
---|
ProteinExtension(boolean onlyPredicted,
ProteinPointLocation position,
String targetAA,
int shift)
Construct
ProteinExtension with the given values |
Modifier and Type | Method and Description |
---|---|
static ProteinExtension |
build(boolean onlyPredicted,
ProteinPointLocation position,
String targetAA,
int shift)
Construct normal
ProteinExtension |
static ProteinExtension |
build(boolean onlyPredicted,
String wtAA,
int pos,
String targetAA,
int shift)
Construct normal
ProteinExtension |
static ProteinExtension |
buildWithoutTerminal(boolean onlyPredicted,
ProteinPointLocation position,
String targetAA)
Construct
ProteinExtension without a terminal in the extension |
static ProteinExtension |
buildWithoutTerminal(boolean onlyPredicted,
String wtAA,
int pos,
String targetAA)
Construct
ProteinExtension without a terminal in the extension |
boolean |
equals(Object obj) |
ProteinPointLocation |
getPosition() |
int |
getShift()
The shift value number of extended amino acids if positive, shift into the 5' UTR in case of negative values, or
LEN_NO_TER in the case that no stop codon is encountered on the transcript. |
String |
getTargetAA() |
int |
hashCode() |
boolean |
isNoTerminalExtension() |
String |
toHGVSString(AminoAcidCode code)
Return HGVS representation using the given amino acid code.
|
String |
toString() |
ProteinChange |
withOnlyPredicted(boolean onlyPredicted) |
isOnlyPredicted, toHGVSString
public static final int LEN_NO_TER
public ProteinExtension(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shift)
ProteinExtension
with the given valuespublic static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift)
ProteinExtension
public static ProteinExtension build(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shift)
ProteinExtension
public static ProteinExtension buildWithoutTerminal(boolean onlyPredicted, String wtAA, int pos, String targetAA)
ProteinExtension
without a terminal in the extensionpublic static ProteinExtension buildWithoutTerminal(boolean onlyPredicted, ProteinPointLocation position, String targetAA)
ProteinExtension
without a terminal in the extensionpublic ProteinPointLocation getPosition()
public String getTargetAA()
public int getShift()
LEN_NO_TER
in the case that no stop codon is encountered on the transcript.public boolean isNoTerminalExtension()
true
if this object describes an extension without a terminal at the endpublic String toHGVSString(AminoAcidCode code)
ConvertibleToHGVSString
code
- AminoAcidCode
to useProteinPointLocation
public int hashCode()
hashCode
in class ProteinChange
public boolean equals(Object obj)
equals
in class ProteinChange
public ProteinChange withOnlyPredicted(boolean onlyPredicted)
withOnlyPredicted
in class ProteinChange
ProteinChange
object with prediction state set to the one given by the parameterCopyright © 2016. All rights reserved.