Package org.snpeff.interval

Class Regulation

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Regulation

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.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, java.lang.String id, java.lang.String name, java.lang.String regulationType)

Method Summary

Modifier and Type	Method	Description
Regulation	cloneShallow()	Perform a shallow clone
java.lang.String	getName()
java.lang.String	getRegulationType()
void	serializeParse(MarkerSerializer markerSerializer)	Parse a line from a serialized file
java.lang.String	serializeSave(MarkerSerializer markerSerializer)	Create a string to serialize to a file
java.lang.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 Detail

Regulation

public Regulation()

Regulation

public Regulation(Marker parent,
                  int start,
                  int end,
                  boolean strandMinus,
                  java.lang.String id,
                  java.lang.String name,
                  java.lang.String regulationType)

Method Detail

cloneShallow

public Regulation cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

getName

public java.lang.String getName()

getRegulationType

public java.lang.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 java.lang.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 java.lang.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