org.snpeff.interval.Regulation

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

public class Regulation extends Marker

Regulatory elements

Author:

pablocingolani

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

Regulation()

Regulation(Marker parent, int start, int end, boolean strandMinus, String id, String name, String regulationType)
Method Summary

Modifier and Type

Method

Description

Regulation

cloneShallow()

Perform a shallow clone

String

getName()

String

getRegulationType()

void

serializeParse(MarkerSerializer markerSerializer)

Parse a line from a serialized file

String

serializeSave(MarkerSerializer markerSerializer)

Create a string to serialize to a file

String

toString()

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, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, 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
- Regulation
  
  public Regulation()
- Regulation
  
  public Regulation(Marker parent, int start, int end, boolean strandMinus, String id, String name, String regulationType)
Method Details
- cloneShallow
  
  public Regulation cloneShallow()
  
  Description copied from class: Marker
  
  Perform a shallow clone
  
  Overrides:
  
  cloneShallow in class Marker
- getName
  
  public String getName()
- getRegulationType
  
  public String getRegulationType()
- serializeParse
  
  public void serializeParse(MarkerSerializer markerSerializer)
  
  Parse a line from a serialized file
  
  Specified by:
  
  serializeParse in interface TxtSerializable
  
  Overrides:
  
  serializeParse in class Marker
- serializeSave
  
  public String serializeSave(MarkerSerializer markerSerializer)
  
  Create a string to serialize to a file
  
  Specified by:
  
  serializeSave in interface TxtSerializable
  
  Overrides:
  
  serializeSave in class Marker
  
  Returns:
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Marker
- variantEffect
  
  public boolean variantEffect(Variant variant, VariantEffects variantEffects)
  
  Calculate the effect of this variant
  
  Overrides:
  
  variantEffect in class Marker

Class Regulation

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

Regulation

Regulation

Method Details

cloneShallow

getName

getRegulationType

serializeParse

serializeSave

toString

variantEffect