Package org.snpeff.interval

Class MicroRnaBindingSite

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.MicroRnaBindingSite

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable

public class MicroRnaBindingSite
extends Marker

miRna binding site (usually this was predicted by some algorithm)

Author:

pcingola

See Also:

Serialized Form

Field Summary

Fields inherited from class org.snpeff.interval.Marker

type

Fields inherited from class org.snpeff.interval.Interval

chromosomeNameOri, end, id, parent, start, strandMinus

Constructor Summary

Constructors

Constructor	Description
MicroRnaBindingSite()
MicroRnaBindingSite(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, double pValue)

Method Summary

Modifier and Type	Method	Description
MicroRnaBindingSite	cloneShallow()	Perform a shallow clone
boolean	variantEffect(Variant variant, VariantEffects changeEffects)	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

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MicroRnaBindingSite

public MicroRnaBindingSite()

MicroRnaBindingSite

public MicroRnaBindingSite(Marker parent,
                           int start,
                           int end,
                           boolean strandMinus,
                           java.lang.String id,
                           double pValue)

Method Detail

cloneShallow

public MicroRnaBindingSite cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects changeEffects)

Description copied from class: Marker

Calculate the effect of this variant

Overrides:

variantEffect in class Marker