public class NucleotideIndel extends NucleotideChange
Constructor and Description |
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NucleotideIndel(boolean onlyPredicted,
NucleotideRange range,
NucleotideSeqDescription delSeq,
NucleotideSeqDescription insSeq) |
Modifier and Type | Method and Description |
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static NucleotideIndel |
buildWithLength(boolean onlyPredicted,
int firstPos,
int lastPos,
int deletedLength,
int insertedLength)
Build without offset and with length information
|
static NucleotideIndel |
buildWithOffsetWithLength(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset,
int deletedLength,
int insertedLength)
Build with length information
|
static NucleotideIndel |
buildWithOffsetWithoutSeqDescription(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset)
Build without any sequence description
|
static NucleotideIndel |
buildWithOffsetWithSeqDescription(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset,
NucleotideSeqDescription delDesc,
NucleotideSeqDescription insDesc)
Build with sequence description
|
static NucleotideIndel |
buildWithOffsetWithSequence(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset,
String deletedSeq,
String insertedSeq)
Build with sequence information
|
static NucleotideIndel |
buildWithoutSeqDescription(boolean onlyPredicted,
int firstPos,
int lastPos)
Build without offset and any sequence description
|
static NucleotideIndel |
buildWithSeqDescription(boolean onlyPredicted,
int firstPos,
int lastPos,
NucleotideSeqDescription delDesc,
NucleotideSeqDescription insDesc)
Build without offset and with sequence description
|
static NucleotideIndel |
buildWithSequence(boolean onlyPredicted,
int firstPos,
int lastPos,
String deletedSeq,
String insertedSeq)
Build without offset and with sequence information
|
boolean |
equals(Object obj) |
NucleotideSeqDescription |
getDelSeq() |
NucleotideSeqDescription |
getInsSeq() |
NucleotideRange |
getRange() |
int |
hashCode() |
String |
toHGVSString()
Return HGVS representation in three-letter amino acid code.
|
String |
toString() |
NucleotideIndel |
withOnlyPredicted(boolean flag) |
isOnlyPredicted, toHGVSString
public NucleotideIndel(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription delSeq, NucleotideSeqDescription insSeq)
public static NucleotideIndel buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset)
public static NucleotideIndel buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, int deletedLength, int insertedLength)
public static NucleotideIndel buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, String deletedSeq, String insertedSeq)
public static NucleotideIndel buildWithOffsetWithSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, NucleotideSeqDescription delDesc, NucleotideSeqDescription insDesc)
public static NucleotideIndel buildWithoutSeqDescription(boolean onlyPredicted, int firstPos, int lastPos)
public static NucleotideIndel buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int deletedLength, int insertedLength)
public static NucleotideIndel buildWithSequence(boolean onlyPredicted, int firstPos, int lastPos, String deletedSeq, String insertedSeq)
public static NucleotideIndel buildWithSeqDescription(boolean onlyPredicted, int firstPos, int lastPos, NucleotideSeqDescription delDesc, NucleotideSeqDescription insDesc)
public NucleotideIndel withOnlyPredicted(boolean flag)
withOnlyPredicted
in class NucleotideChange
NucleotideChange
with given onlyPredicted
value.public String toHGVSString()
ConvertibleToHGVSString
ProteinPointLocation
public NucleotideRange getRange()
public NucleotideSeqDescription getInsSeq()
public NucleotideSeqDescription getDelSeq()
public int hashCode()
hashCode
in class NucleotideChange
public boolean equals(Object obj)
equals
in class NucleotideChange
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