Package org.snpeff.interval

Class Motif

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Motif

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable

public class Motif
extends Marker

Regulatory elements

Author:

pablocingolani

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug
static double	SCORE_THRESHOLD

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
Motif()
Motif(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String pwmName, java.lang.String pwmId)

Method Summary

Modifier and Type	Method	Description
Motif	cloneShallow()	Perform a shallow clone
Pwm	getPwm()
java.lang.String	getPwmId()
java.lang.String	getPwmName()
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
void	setPwm(Pwm pwm)
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, 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

Field Detail

SCORE_THRESHOLD

public static final double SCORE_THRESHOLD

See Also:

Constant Field Values

debug

public static final boolean debug

See Also:

Constant Field Values

Constructor Detail

Motif

public Motif()

Motif

public Motif(Marker parent,
             int start,
             int end,
             boolean strandMinus,
             java.lang.String id,
             java.lang.String pwmName,
             java.lang.String pwmId)

Method Detail

cloneShallow

public Motif cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

getPwm

public Pwm getPwm()

getPwmId

public java.lang.String getPwmId()

getPwmName

public java.lang.String getPwmName()

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Description copied from class: Marker

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

setPwm

public void setPwm(Pwm pwm)

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects variantEffects)

Calculate the effect of this variant

Overrides:

variantEffect in class Marker