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:

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

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 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, toString, union, variantEffect, 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 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)

Class GenericMarker

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

Constructor Details

GenericMarker

GenericMarker

Method Details

cloneShallow

getLine

setLine