Package org.snpsift.annotate

Class MarkerFile

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.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:
    Serialized Form

    • 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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      long getFileIdx()  
      java.lang.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 Detail

      • fileIdx

        protected long fileIdx

    • Constructor Detail

      • MarkerFile

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

    • Method Detail

      • getFileIdx

        public long getFileIdx()

      • toString

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