Package org.snpsift.annotate

Class MarkerFile

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpsift.annotate.MarkerFile
All Implemented Interfaces:
Serializable, Cloneable, Comparable<org.snpeff.interval.Interval>, org.snpeff.serializer.TxtSerializable
public class MarkerFile extends org.snpeff.interval.Marker
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
Author:
pcingola
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected long
    fileIdx
     

    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
    MarkerFile(org.snpeff.interval.Marker parent, int start, int end, long fileIdx)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    long
    getFileIdx()
     
    String
    toString()
     

    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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, 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

  • Field Details

    • fileIdx

      protected long fileIdx

  • Constructor Details

    • MarkerFile

      public MarkerFile(org.snpeff.interval.Marker parent, int start, int end, long fileIdx)

  • Method Details

    • getFileIdx

      public long getFileIdx()

    • toString

      public String toString()
      Overrides:
      toString in class org.snpeff.interval.Marker