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:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class ProteinProteinInteractionLocus extends ProteinInteractionLocus
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:
- Serialized Form
-
-
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
-
-
Constructor Summary
Constructors Constructor Description ProteinProteinInteractionLocus()
ProteinProteinInteractionLocus(Transcript parent, int start, int end, Transcript trInteract, java.lang.String id)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ProteinProteinInteractionLocus
cloneShallow()
Perform a shallow cloneboolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant-
Methods 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
-
-
-
-
Constructor Detail
-
ProteinProteinInteractionLocus
public ProteinProteinInteractionLocus()
-
ProteinProteinInteractionLocus
public ProteinProteinInteractionLocus(Transcript parent, int start, int end, Transcript trInteract, java.lang.String id)
-
-
Method Detail
-
cloneShallow
public ProteinProteinInteractionLocus cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classProteinInteractionLocus
-
variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant- Overrides:
variantEffect
in classProteinInteractionLocus
-
-