Class Field

java.lang.Object
org.snpsift.lang.expression.Expression
org.snpsift.lang.expression.Field
Direct Known Subclasses:
FieldConstant, FieldSub

public class Field extends Expression
A field: E.g.: 'DP', 'CHROM'
Author:
pablocingolani
  • Field Details

    • TYPE_ALL

      public static final int TYPE_ALL
      See Also:
    • TYPE_ANY

      public static final int TYPE_ANY
      See Also:
    • name

      protected String name
    • returnType

      protected org.snpeff.vcf.VcfInfoType returnType
    • exceptionIfNotFound

      protected boolean exceptionIfNotFound
    • vcfInfo

      protected org.snpeff.vcf.VcfHeaderInfo vcfInfo
    • number

      protected int number
    • vcfInfoNumber

      protected org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber vcfInfoNumber
  • Constructor Details

    • Field

      public Field(String name)
  • Method Details

    • eval

      public Value eval(org.snpeff.vcf.VcfEntry vcfEntry)
      Description copied from class: Expression
      Evaluate expression using VcfEntry
      Specified by:
      eval in class Expression
    • eval

      public Value eval(org.snpeff.vcf.VcfGenotype vcfGenotype)
      Description copied from class: Expression
      Evaluate expression using genotype
      Specified by:
      eval in class Expression
    • fieldHeaderNotFound

      protected Object fieldHeaderNotFound(org.snpeff.vcf.VcfEntry vcfEntry)
    • fieldNotFound

      protected Object fieldNotFound(org.snpeff.vcf.VcfEntry vcfEntry)
    • getFieldString

      public String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
    • getName

      public String getName()
    • getReturnType

      public org.snpeff.vcf.VcfInfoType getReturnType(org.snpeff.vcf.VcfGenotype vcfGenotype)
    • getSampleNum

      protected int getSampleNum(org.snpeff.vcf.VcfEntry vcfEntry, String name)
    • gtFieldNotFound

      protected Object gtFieldNotFound(org.snpeff.vcf.VcfGenotype vcfGenotype)
    • indexStr

      public String indexStr(int index)
      Convert and index to a string
    • isSampleName

      protected boolean isSampleName(org.snpeff.vcf.VcfEntry vcfEntry, String name)
    • isSub

      protected boolean isSub()
    • returnType

      public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfEntry vcfEntry)
    • returnType

      public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfGenotype vcfGenotype)
    • setExceptionIfNotFound

      public void setExceptionIfNotFound(boolean exceptionIfNotFound)
    • toString

      public String toString()
      Overrides:
      toString in class Object