GenericMarker (SnpEff 5.4 API)

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.GenericMarker

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

public class GenericMarker extends Marker

An interval intended as a mark

Author:

pcingola

See Also:

Field Summary

Fields inherited from class Marker
type

Fields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus
Constructor Summary

Constructors

Constructor

Description

GenericMarker()

GenericMarker(Marker parent, int start, int end, String id)
Method Summary

Modifier and Type

Method

Description

GenericMarker

cloneShallow()

Perform a shallow clone

String

getLine()

void

setLine(String line)

Methods inherited from class 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, toString, union, variantEffect, variantEffectNonRef

Methods inherited from class 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 Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details
- GenericMarker
  
  public GenericMarker()
- GenericMarker
  
  public GenericMarker(Marker parent, int start, int end, String id)
Method Details
- cloneShallow
  
  public GenericMarker cloneShallow()
  
  Description copied from class: Marker
  
  Perform a shallow clone
  
  Overrides:
  
  cloneShallow in class Marker
- getLine
  
  public String getLine()
- setLine
  
  public void setLine(String line)