Class SingleAlleleProteinVariant
- java.lang.Object
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- de.charite.compbio.jannovar.hgvs.HGVSVariant
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- de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant
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- de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant
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- All Implemented Interfaces:
ConvertibleToHGVSString
public class SingleAlleleProteinVariant extends ProteinVariant
Protein change with one allele only.- Author:
- Manuel Holtgrewe
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Field Summary
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Fields inherited from class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant
NO_PROTEIN_ISOFORM
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Constructor Summary
Constructors Constructor Description SingleAlleleProteinVariant(String proteinID, VariantConfiguration varConfig, Collection<? extends ProteinChange> changes)
ConstructSingleAlleleProteinVariant
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static SingleAlleleProteinVariant
build(String proteinID, VariantConfiguration varConfig, ProteinChange... changes)
boolean
equals(Object obj)
ProteinChangeAllele
getAllele()
ProteinChange
getChange()
int
hashCode()
boolean
hasOnlyOneChange()
static SingleAlleleProteinVariant
makeSingleChangeVariant(String proteinID, ProteinChange change)
String
toHGVSString(AminoAcidCode code)
Return HGVS representation using the given amino acid code.String
toString()
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Methods inherited from class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant
getProteinID, getSequenceNamePrefix, toHGVSString
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Constructor Detail
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SingleAlleleProteinVariant
public SingleAlleleProteinVariant(String proteinID, VariantConfiguration varConfig, Collection<? extends ProteinChange> changes)
ConstructSingleAlleleProteinVariant
- Parameters:
proteinID
- ID of the protein that the change is onvarConfig
-VariantConfiguration
of theProteinChange
s in the allelechanges
-ProteinChange
s to use for the single allele
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Method Detail
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makeSingleChangeVariant
public static SingleAlleleProteinVariant makeSingleChangeVariant(String proteinID, ProteinChange change)
- Returns:
- protein variant for one change only
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build
public static SingleAlleleProteinVariant build(String proteinID, VariantConfiguration varConfig, ProteinChange... changes)
- Returns:
- single-change
SingleAlleleProteinVariant
with the given protein ID andVariantConfiguration
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hasOnlyOneChange
public boolean hasOnlyOneChange()
- Returns:
true
if the variant has only oneProteinChange
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getChange
public ProteinChange getChange()
- Returns:
- first change, convenience method for single-change variants
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getAllele
public ProteinChangeAllele getAllele()
- Returns:
- list of changes
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toHGVSString
public String toHGVSString(AminoAcidCode code)
Description copied from interface:ConvertibleToHGVSString
Return HGVS representation using the given amino acid code.- Parameters:
code
-AminoAcidCode
to use- Returns:
- HGVS representation, e.g. "133L" for an
ProteinPointLocation
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toString
public String toString()
- Overrides:
toString
in classProteinVariant
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hashCode
public int hashCode()
- Overrides:
hashCode
in classProteinVariant
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equals
public boolean equals(Object obj)
- Overrides:
equals
in classProteinVariant
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