org.snpeff.interval.SpliceSiteBranch

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

Direct Known Subclasses:: SpliceSiteBranchU12

public class SpliceSiteBranch extends SpliceSite

A (putative) branch site.

Author:

pablocingolani

See Also:

Serialized Form

Field Summary

Fields inherited from class org.snpeff.interval.SpliceSite
CORE_SPLICE_SITE_SIZE, SPLICE_REGION_EXON_SIZE, SPLICE_REGION_INTRON_MAX, SPLICE_REGION_INTRON_MIN

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

SpliceSiteBranch()

SpliceSiteBranch(Intron parent, int start, int end, boolean strandMinus, String id)
Method Summary

Modifier and Type

Method

Description

boolean

intersectsCoreSpliceSite(Marker marker)

These are NOT core splice sites

Methods inherited from class org.snpeff.interval.SpliceSite
isShowWarningIfParentDoesNotInclude, variantEffect

Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, query, readTxt, serializeParse, serializeSave, 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

Constructor Details
- SpliceSiteBranch
  
  public SpliceSiteBranch()
- SpliceSiteBranch
  
  public SpliceSiteBranch(Intron parent, int start, int end, boolean strandMinus, String id)
Method Details
- intersectsCoreSpliceSite
  
  public boolean intersectsCoreSpliceSite(Marker marker)
  
  These are NOT core splice sites
  
  Specified by:
  
  intersectsCoreSpliceSite in class SpliceSite

Class SpliceSiteBranch

Field Summary

Fields inherited from class org.snpeff.interval.SpliceSite

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.SpliceSite

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

SpliceSiteBranch

SpliceSiteBranch

Method Details

intersectsCoreSpliceSite