Package org.snpsift.fileIterator

Class DbNsfpEntry

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<org.snpeff.interval.Interval>, org.snpeff.serializer.TxtSerializable
    public class DbNsfpEntry
extends org.snpeff.interval.Variant
    DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs
    Author:
    lletourn
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from class org.snpeff.interval.Variant

        org.snpeff.interval.Variant.VariantType

    • Field Summary

      • Fields inherited from class org.snpeff.interval.Variant

        alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType

      • 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
      DbNsfpEntry​(DbNsfp dbNsfp, java.lang.String line)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(java.lang.String columnName, java.lang.String valuesToAdd)
      Add a value
      DbNsfpEntry cloneShallow()  
      java.lang.String getVcfInfo​(java.lang.String key)
      Get data in a VCF INFO field compatible format
      boolean hasValues​(java.lang.String allele)
      Do we have values for this allele
      protected void parseChrPosRefAlt()
      Parse dbSNFP 'Chr, pos, ref, alt' values from a single line
      protected void parseKeyValues()
      Parse dbSNFP ALL values from a single line and store them in 'values' hash
      int parsePosition​(java.lang.String posStr)
      Parse a string as a 'position'.
      static java.lang.String[] splitValuesField​(java.lang.String value)  
      java.lang.String toString()  

      • Methods inherited from class org.snpeff.interval.Variant

        clone, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, realignLeft, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld

      • Methods inherited from class org.snpeff.interval.Marker

        adjust, apply, applyDel, applyDup, applyIns, applyMixed, codonTable, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, 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, 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 Detail

      • DbNsfpEntry

        public DbNsfpEntry​(DbNsfp dbNsfp,
                   java.lang.String line)

    • Method Detail

      • splitValuesField

        public static java.lang.String[] splitValuesField​(java.lang.String value)

      • add

        public void add​(java.lang.String columnName,
                java.lang.String valuesToAdd)
        Add a value

      • cloneShallow

        public DbNsfpEntry cloneShallow()
        Overrides:
        cloneShallow in class org.snpeff.interval.Variant

      • getVcfInfo

        public java.lang.String getVcfInfo​(java.lang.String key)
        Get data in a VCF INFO field compatible format

      • hasValues

        public boolean hasValues​(java.lang.String allele)
        Do we have values for this allele

      • parseChrPosRefAlt

        protected void parseChrPosRefAlt()
        Parse dbSNFP 'Chr, pos, ref, alt' values from a single line

      • parseKeyValues

        protected void parseKeyValues()
        Parse dbSNFP ALL values from a single line and store them in 'values' hash

        Note: This method is supposed to be a lazy parsing of the key/value pairs, so it DOES NOT store 'chr, pos, ref, alt'. You can use `parseChrPosRefAlt()` for that.

      • parsePosition

        public int parsePosition​(java.lang.String posStr)
        Parse a string as a 'position'.

      • toString

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