Utr (SnpEff 5.4 API)

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Utr

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

Direct Known Subclasses:: Utr3prime, Utr5prime

public abstract class Utr extends Marker

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

Author:

pcingola

See Also:

Field Summary

Fields inherited from class Marker
type

Fields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus
Constructor Summary

Constructors

Constructor

Description

Utr()

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

Modifier and Type

Method

Description

abstract boolean

isUtr3prime()

abstract boolean

isUtr5prime()

Methods inherited from class 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, variantEffect, variantEffectNonRef

Methods inherited from class 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 Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details
- Utr
  
  public Utr()
- Utr
  
  public Utr(Exon parent, int start, int end, boolean strandMinus, String id)
Method Details
- isUtr3prime
  
  public abstract boolean isUtr3prime()
- isUtr5prime
  
  public abstract boolean isUtr5prime()