Package org.snpeff.interval
Class ProteinInteractionLocus
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.ProteinInteractionLocus
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
ProteinProteinInteractionLocus
,ProteinStructuralInteractionLocus
public abstract class ProteinInteractionLocus extends Marker
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:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description ProteinInteractionLocus()
ProteinInteractionLocus(Transcript parent, int start, int end, java.lang.String id)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description ProteinInteractionLocus
cloneShallow()
Perform a shallow clonestatic java.util.List<ProteinInteractionLocus>
factory(Transcript tr, int aaPos, Transcript trInteract, java.lang.String id)
Create interaction.boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant-
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
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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 Detail
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debug
public static final boolean debug
- See Also:
- Constant Field Values
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Constructor Detail
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ProteinInteractionLocus
public ProteinInteractionLocus()
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ProteinInteractionLocus
public ProteinInteractionLocus(Transcript parent, int start, int end, java.lang.String id)
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Method Detail
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factory
public static java.util.List<ProteinInteractionLocus> factory(Transcript tr, int aaPos, Transcript trInteract, java.lang.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
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cloneShallow
public ProteinInteractionLocus cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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