public class ProteinFrameshift extends ProteinChange
Modifier and Type | Field and Description |
---|---|
static int |
LEN_NO_TER
no terminal is encountered
|
static int |
LEN_SHORT
short change description
|
Constructor and Description |
---|
ProteinFrameshift(boolean onlyPredicted,
ProteinPointLocation position,
String targetAA,
int shiftLength)
Construct
ProteinFrameshift with the given values |
Modifier and Type | Method and 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) |
isOnlyPredicted, toHGVSString
public static final int LEN_NO_TER
public static final int LEN_SHORT
public ProteinFrameshift(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shiftLength)
ProteinFrameshift
with the given valuespublic static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength)
ProteinFrameshift
with full settingspublic static ProteinFrameshift build(boolean onlyPredicted, ProteinPointLocation position, String targetAA, int shiftLength)
ProteinFrameshift
with full settingspublic static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position)
ProteinFrameshift
short descriptionpublic static ProteinFrameshift buildShort(boolean onlyPredicted, ProteinPointLocation position)
ProteinFrameshift
short descriptionpublic static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA)
ProteinFrameshift
for the case that there is no terminalpublic static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, ProteinPointLocation position, String targetAA)
ProteinFrameshift
for the case that there is no terminalpublic boolean isShort()
true
if this object is a short description of a frame shift.public boolean isNoTerminalFrameshfit()
true
if this object describes a frameshift without a terminal at the endpublic ProteinPointLocation getPosition()
public String getTargetAA()
null
if this is a short descriptionpublic int getShiftLength()
public 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.