Class ProteinInsertion
- 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.ProteinInsertion
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- All Implemented Interfaces:
ConvertibleToHGVSString
public class ProteinInsertion extends ProteinChange
Insertion into a protein sequence.- Author:
- Manuel Holtgrewe
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Constructor Summary
Constructors Constructor Description ProteinInsertion(boolean onlyPredicted, ProteinRange position, ProteinSeqDescription seq)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static ProteinInsertion
buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
Build without any sequence description.static ProteinInsertion
buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int insertedLength)
Build with length informationstatic ProteinInsertion
buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
Build without any SeqDescriptionstatic ProteinInsertion
buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription seqDescription)
Build with SeqDescriptionstatic ProteinInsertion
buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)
Build with sequenceboolean
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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ProteinInsertion
public ProteinInsertion(boolean onlyPredicted, ProteinRange position, ProteinSeqDescription seq)
- Parameters:
onlyPredicted
- whether the change was only predictedposition
- range of length one giving the insertion positionseq
- description of the inserted sequence
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Method Detail
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buildWithLength
public static ProteinInsertion buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
Build without any sequence description.
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buildWithLength
public static ProteinInsertion buildWithLength(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, int insertedLength)
Build with length information
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buildWithSequence
public static ProteinInsertion buildWithSequence(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, String seq)
Build with sequence
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buildWithSeqDescription
public static ProteinInsertion buildWithSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos, ProteinSeqDescription seqDescription)
Build with SeqDescription
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buildWithoutSeqDescription
public static ProteinInsertion buildWithoutSeqDescription(boolean onlyPredicted, String firstAA, int firstPos, String lastAA, int lastPos)
Build without any SeqDescription
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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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