org.snpeff.interval.Downstream

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

public class Downstream extends Marker

Interval for a gene, as well as some other information: exons, utrs, cds, etc.

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

Downstream()

Downstream(Transcript parent, int start, int end, boolean strandMinus, String id)
Method Summary

Modifier and Type

Method

Description

int

distanceToTr(Variant variant)

Distance to transcript

protected boolean

isShowWarningIfParentDoesNotInclude()

Upstream sites are no included in transcript (by definition).

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, 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
- Downstream
  
  public Downstream()
- Downstream
  
  public Downstream(Transcript parent, int start, int end, boolean strandMinus, String id)
Method Details
- distanceToTr
  
  public int distanceToTr(Variant variant)
  
  Distance to transcript
- isShowWarningIfParentDoesNotInclude
  
  protected boolean isShowWarningIfParentDoesNotInclude()
  
  Upstream sites are no included in transcript (by definition).
  
  Overrides:
  
  isShowWarningIfParentDoesNotInclude in class Marker
- 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 Downstream

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

Downstream

Downstream

Method Details

distanceToTr

isShowWarningIfParentDoesNotInclude

variantEffect