Package org.snpeff.interval
Class ProteinProteinInteractionLocus
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.ProteinInteractionLocus
org.snpeff.interval.ProteinProteinInteractionLocus
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Protein interaction: An amino acid that is "in contact" with another amino acid
within the same protein. Evidence form PDB crystallized structures
- Author:
- pablocingolani
- See Also:
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Field Summary
Fields inherited from class org.snpeff.interval.ProteinInteractionLocus
debug
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionProteinProteinInteractionLocus
(Transcript parent, int start, int end, Transcript trInteract, String id) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow cloneboolean
variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantMethods inherited from class org.snpeff.interval.ProteinInteractionLocus
factory
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
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Constructor Details
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ProteinProteinInteractionLocus
public ProteinProteinInteractionLocus() -
ProteinProteinInteractionLocus
public ProteinProteinInteractionLocus(Transcript parent, int start, int end, Transcript trInteract, String id)
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Method Details
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cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classProteinInteractionLocus
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variantEffect
Calculate the effect of this variant- Overrides:
variantEffect
in classProteinInteractionLocus
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