Package org.snpeff.interval
Class ProteinInteractionLocus
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.ProteinInteractionLocus
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
ProteinProteinInteractionLocus
,ProteinStructuralInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.
This can be either within the same protein or interacting with another protein.
Evidence form PDB crystallized structures
- Author:
- pablocingolani
- See Also:
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Field Summary
FieldsFields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonestatic List
<ProteinInteractionLocus> factory
(Transcript tr, int aaPos, Transcript trInteract, String id) Create interaction.boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantMethods 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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Field Details
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debug
public static final boolean debug- See Also:
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Constructor Details
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ProteinInteractionLocus
public ProteinInteractionLocus() -
ProteinInteractionLocus
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Method Details
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factory
public static List<ProteinInteractionLocus> factory(Transcript tr, int aaPos, Transcript trInteract, String id) Create interaction. Most of the time it is only one interval, but if introns split an amino acid, it may be more then one interval -
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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variantEffect
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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