public class SingleAlleleNucleotideVariant extends NucleotideVariant
NO_TRANSCRIPT_VERSION
Constructor and Description |
---|
SingleAlleleNucleotideVariant(SequenceType seqType,
String seqID,
NucleotideChangeAllele allele)
Construct
SingleAlleleNucleotideVariant |
SingleAlleleNucleotideVariant(SequenceType seqType,
String refID,
String proteinID,
int transcriptVersion,
NucleotideChangeAllele allele)
Construct
SingleAlleleNucleotideVariant |
SingleAlleleNucleotideVariant(SequenceType seqType,
String seqID,
VariantConfiguration varConfig,
Collection<? extends NucleotideChange> changes)
Construct
SingleAlleleNucleotideVariant |
Modifier and Type | Method and Description |
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static SingleAlleleNucleotideVariant |
build(SequenceType seqType,
String seqID,
VariantConfiguration varConfig,
NucleotideChange... changes) |
boolean |
equals(Object obj) |
NucleotideChangeAllele |
getAllele() |
NucleotideChange |
getChange() |
int |
hashCode() |
boolean |
hasOnlyOneChange() |
static SingleAlleleNucleotideVariant |
makeSingleChangeVariant(SequenceType seqType,
String seqID,
NucleotideChange change) |
String |
toHGVSString()
Return HGVS representation in three-letter amino acid code.
|
getProteinID, getRefID, getRefIDWithVersion, getSeqType, getSequenceNamePrefix, getTranscriptVersion, toHGVSString, toString
public SingleAlleleNucleotideVariant(SequenceType seqType, String seqID, VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes)
SingleAlleleNucleotideVariant
seqType
- type of the changed sequenceseqID
- ID of the reference/transcript that the change is onvarConfig
- VariantConfiguration
of the NucleotideChange
s in the allelechanges
- NucleotideChange
s to use for the single allelepublic SingleAlleleNucleotideVariant(SequenceType seqType, String refID, String proteinID, int transcriptVersion, NucleotideChangeAllele allele)
SingleAlleleNucleotideVariant
public SingleAlleleNucleotideVariant(SequenceType seqType, String seqID, NucleotideChangeAllele allele)
SingleAlleleNucleotideVariant
seqType
- type of the changed sequenceseqID
- ID of the reference/transcript that the change is onallele
- NucleotideChangeAllele
to usepublic static SingleAlleleNucleotideVariant makeSingleChangeVariant(SequenceType seqType, String seqID, NucleotideChange change)
public static SingleAlleleNucleotideVariant build(SequenceType seqType, String seqID, VariantConfiguration varConfig, NucleotideChange... changes)
SingleAlleleNucleotideVariant
with the given SequenceType
,
reference/transcript ID, and VariantConfiguration
public boolean hasOnlyOneChange()
true
if the variant has only one NucleotideChange
.public NucleotideChange getChange()
public NucleotideChangeAllele getAllele()
public String toHGVSString()
ConvertibleToHGVSString
ProteinPointLocation
public int hashCode()
hashCode
in class NucleotideVariant
public boolean equals(Object obj)
equals
in class NucleotideVariant
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