public class NucleotideInsertion extends NucleotideChange
Constructor and Description |
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NucleotideInsertion(boolean onlyPredicted,
NucleotideRange position,
NucleotideSeqDescription seq) |
Modifier and Type | Method and Description |
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static NucleotideInsertion |
buildWithLength(boolean onlyPredicted,
int firstPos,
int lastPos)
Build without offset and no sequence description
|
static NucleotideInsertion |
buildWithLength(boolean onlyPredicted,
int firstPos,
int lastPos,
int insertedLength)
Build without offset and with length information
|
static NucleotideInsertion |
buildWithOffsetWithLength(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset,
int insertedLength)
Build with length information
|
static NucleotideInsertion |
buildWithOffsetWithoutSeqDescription(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset)
Build without any sequence description
|
static NucleotideInsertion |
buildWithOffsetWithSequence(boolean onlyPredicted,
int firstPos,
int firstOffset,
int lastPos,
int lastOffset,
String seq)
Build with sequence
|
static NucleotideInsertion |
buildWithSequence(boolean onlyPredicted,
int firstPos,
int lastPos,
String seq)
Build without offset and with sequence
|
boolean |
equals(Object obj) |
NucleotideRange |
getRange() |
NucleotideSeqDescription |
getSeq() |
int |
hashCode() |
String |
toHGVSString()
Return HGVS representation in three-letter amino acid code.
|
String |
toString() |
NucleotideInsertion |
withOnlyPredicted(boolean flag) |
isOnlyPredicted, toHGVSString
public NucleotideInsertion(boolean onlyPredicted, NucleotideRange position, NucleotideSeqDescription seq)
onlyPredicted
- whether the change was only predictedposition
- range of length one giving the insertion positionseq
- description of the inserted sequencepublic static NucleotideInsertion buildWithOffsetWithoutSeqDescription(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionfirstOffset
- offset for begin position of insertionlastPos
- end position of insertionlastOffset
- offset for end position of insertionNucleotideInsertion
public static NucleotideInsertion buildWithOffsetWithLength(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, int insertedLength)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionfirstOffset
- offset for begin position of insertionlastPos
- end position of insertionlastOffset
- offset for end position of insertioninsertedLength
- the number of inserted basesNucleotideInsertion
public static NucleotideInsertion buildWithOffsetWithSequence(boolean onlyPredicted, int firstPos, int firstOffset, int lastPos, int lastOffset, String seq)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionfirstOffset
- offset for begin position of insertionlastPos
- end position of insertionlastOffset
- offset for end position of insertionseq
- the inserted sequenceNucleotideInsertion
public static NucleotideInsertion buildWithLength(boolean onlyPredicted, int firstPos, int lastPos)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionlastPos
- end position of insertionNucleotideInsertion
public static NucleotideInsertion buildWithLength(boolean onlyPredicted, int firstPos, int lastPos, int insertedLength)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionlastPos
- end position of insertioninsertedLength
- the number of inserted basesNucleotideInsertion
public static NucleotideInsertion buildWithSequence(boolean onlyPredicted, int firstPos, int lastPos, String seq)
onlyPredicted
- whether or not to add marker for "only predicted"firstPos
- begin position of insertionlastPos
- end position of insertionseq
- the inserted sequenceNucleotideInsertion
public NucleotideRange getRange()
public NucleotideSeqDescription getSeq()
public NucleotideInsertion withOnlyPredicted(boolean flag)
withOnlyPredicted
in class NucleotideChange
NucleotideChange
with given onlyPredicted
value.public String toHGVSString()
ConvertibleToHGVSString
ProteinPointLocation
public int hashCode()
hashCode
in class NucleotideChange
public boolean equals(Object obj)
equals
in class NucleotideChange
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