Package org.snpeff.ped

Class PedGenotype

  • public class PedGenotype
extends java.lang.Object
    A Simple genotype implementation for PED files
    Author:
    pcingola

    • Constructor Summary

      Constructors 
      Constructor Description
      PedGenotype​(java.lang.String[] genotypes)  
      PedGenotype​(java.lang.String[] genotypes, java.lang.String chrName, int position)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String get​(int idx)  
      java.lang.String[] getGenotypes()  
      int getPosition()  
      boolean has​(java.lang.String genotype)
      Is 'genotype' in this one?
      boolean isHomozygous()
      Is this homozygous?
      boolean isValid()  
      int size()  
      java.lang.String toString()  
      java.lang.String toString​(boolean wcComplement)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • PedGenotype

        public PedGenotype​(java.lang.String[] genotypes)

      • PedGenotype

        public PedGenotype​(java.lang.String[] genotypes,
                   java.lang.String chrName,
                   int position)

    • Method Detail

      • get

        public java.lang.String get​(int idx)

      • getGenotypes

        public java.lang.String[] getGenotypes()

      • getPosition

        public int getPosition()

      • has

        public boolean has​(java.lang.String genotype)
        Is 'genotype' in this one?
        Parameters:
        genotype -
        Returns:

      • isHomozygous

        public boolean isHomozygous()
        Is this homozygous?
        Returns:

      • isValid

        public boolean isValid()

      • size

        public int size()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toString

        public java.lang.String toString​(boolean wcComplement)