Class ProteinDuplication
- java.lang.Object
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- de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange
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- de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication
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- All Implemented Interfaces:
ConvertibleToHGVSString
public class ProteinDuplication extends ProteinChange
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Constructor Summary
Constructors Constructor Description ProteinDuplication(boolean onlyPredicted, ProteinRange range, ProteinSeqDescription seqSpec)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static ProteinDuplication
buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int len)
static ProteinDuplication
buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
static ProteinDuplication
buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription desc)
static ProteinDuplication
buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)
boolean
equals(Object obj)
int
hashCode()
String
toHGVSString(AminoAcidCode code)
Return HGVS representation using the given amino acid code.String
toString()
ProteinChange
withOnlyPredicted(boolean onlyPredicted)
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Methods inherited from class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange
isOnlyPredicted, toHGVSString
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Constructor Detail
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ProteinDuplication
public ProteinDuplication(boolean onlyPredicted, ProteinRange range, ProteinSeqDescription seqSpec)
- Parameters:
onlyPredicted
-range
-seqSpec
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Method Detail
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buildWithoutSeqDescription
public static ProteinDuplication buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
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buildWithSequence
public static ProteinDuplication buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)
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buildWithLength
public static ProteinDuplication buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int len)
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buildWithSeqDescription
public static ProteinDuplication buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription desc)
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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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hashCode
public int hashCode()
- Overrides:
hashCode
in classProteinChange
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equals
public boolean equals(Object obj)
- Overrides:
equals
in classProteinChange
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withOnlyPredicted
public ProteinChange withOnlyPredicted(boolean onlyPredicted)
- Specified by:
withOnlyPredicted
in classProteinChange
- Returns:
ProteinChange
object with prediction state set to the one given by the parameter
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