org.snpeff.interval.Custom

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

Direct Known Subclasses:: GffMarker

public class Custom extends Marker implements Iterable<KeyValue<String,String>>

This is a custom interval (i.e. intervals provided by the user)

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

Custom()

Custom(Marker parent, int start, int end, boolean strandMinus, String id, String label)
Method Summary

Modifier and Type

Method

Description

Custom

cloneShallow()

Perform a shallow clone

String

getLabel()

double

getScore()

boolean

hasAnnotations()

Do we have additional annotations?

Iterator<KeyValue<String,String>>

iterator()

void

setLabel(String label)

void

setScore(double score)

String

toString()

boolean

variantEffect(Variant variant, VariantEffects changeEffecs)

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, serializeParse, serializeSave, 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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- Custom
  
  public Custom()
- Custom
  
  public Custom(Marker parent, int start, int end, boolean strandMinus, String id, String label)
Method Details
- cloneShallow
  
  public Custom cloneShallow()
  
  Description copied from class: Marker
  
  Perform a shallow clone
  
  Overrides:
  
  cloneShallow in class Marker
- getLabel
  
  public String getLabel()
- getScore
  
  public double getScore()
- hasAnnotations
  
  public boolean hasAnnotations()
  
  Do we have additional annotations?
- iterator
  
  public Iterator<KeyValue<String,String>> iterator()
  
  Specified by:
  
  iterator in interface Iterable<KeyValue<String,String>>
- setLabel
  
  public void setLabel(String label)
- setScore
  
  public void setScore(double score)
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Marker
- variantEffect
  
  public boolean variantEffect(Variant variant, VariantEffects changeEffecs)
  
  Description copied from class: Marker
  
  Calculate the effect of this variant
  
  Overrides:
  
  variantEffect in class Marker

Class Custom

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

Methods inherited from interface java.lang.Iterable

Constructor Details

Custom

Custom

Method Details

cloneShallow

getLabel

getScore

hasAnnotations

iterator

setLabel

setScore

toString

variantEffect