org.snpeff.interval.Utr3prime

All Implemented Interfaces:: Serializable, Cloneable, Comparable<Interval>, TxtSerializable

public class Utr3prime extends Utr

Interval for a UTR (5 prime UTR and 3 prime UTR

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

Utr3prime()

Utr3prime(Exon parent, int start, int end, boolean strandMinus, String id)
Method Summary

Modifier and Type

Method

Description

boolean

isUtr3prime()

boolean

isUtr5prime()

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, cloneShallow, 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 Details
- Utr3prime
  
  public Utr3prime()
- Utr3prime
  
  public Utr3prime(Exon parent, int start, int end, boolean strandMinus, String id)
Method Details
- isUtr3prime
  
  public boolean isUtr3prime()
  
  Specified by:
  
  isUtr3prime in class Utr
- isUtr5prime
  
  public boolean isUtr5prime()
  
  Specified by:
  
  isUtr5prime in class Utr
- variantEffect
  
  public boolean variantEffect(Variant variant, VariantEffects variantEffects)
  
  Description copied from class: Marker
  
  Calculate the effect of this variant
  
  Overrides:
  
  variantEffect in class Marker

Class Utr3prime

Field Summary

Fields inherited from class org.snpeff.interval.Marker

Fields inherited from class org.snpeff.interval.Interval

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.interval.Marker

Methods inherited from class org.snpeff.interval.Interval

Methods inherited from class java.lang.Object

Constructor Details

Utr3prime

Utr3prime

Method Details

isUtr3prime

isUtr5prime

variantEffect