org.snpeff.interval.Motif

All Implemented Interfaces:: Serializable, Cloneable, 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 final boolean

debug

static final 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, String id, String pwmName, String pwmId)
Method Summary

Modifier and Type

Method

Description

Motif

cloneShallow()

Perform a shallow clone

Pwm

getPwm()

String

getPwmId()

String

getPwmName()

void

serializeParse(MarkerSerializer markerSerializer)

Parse a line from a serialized file

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 Details
- 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 Details
- Motif
  
  public Motif()
- Motif
  
  public Motif(Marker parent, int start, int end, boolean strandMinus, String id, String pwmName, String pwmId)
Method Details
- cloneShallow
  
  public Motif cloneShallow()
  
  Description copied from class: Marker
  
  Perform a shallow clone
  
  Overrides:
  
  cloneShallow in class Marker
- getPwm
  
  public Pwm getPwm()
- getPwmId
  
  public String getPwmId()
- getPwmName
  
  public 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 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

Class Motif

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

Field Details

SCORE_THRESHOLD

debug

Constructor Details

Motif

Motif

Method Details

cloneShallow

getPwm

getPwmId

getPwmName

serializeParse

serializeSave

setPwm

variantEffect