Package org.snpsift.lang.expression

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