Package org.snpeff.ped

Class PedPedigree

  • All Implemented Interfaces:
    java.lang.Comparable<PedPedigree>, java.lang.Iterable<TfamEntry>
    Direct Known Subclasses:
    PedFamily
    public class PedPedigree
extends java.lang.Object
implements java.lang.Iterable<TfamEntry>, java.lang.Comparable<PedPedigree>
    A pedigree of PedEntries
    Author:
    pcingola

    • Constructor Summary

      Constructors 
      Constructor Description
      PedPedigree()  
      PedPedigree​(java.lang.String tfamFileName)  

    • Constructor Detail

      • PedPedigree

        public PedPedigree()

      • PedPedigree

        public PedPedigree​(java.lang.String tfamFileName)

    • Method Detail

      • add

        public void add​(TfamEntry tfamEntry)
        Add an entry to this pedigree
        Parameters:
        tfamEntry -

      • compareTo

        public int compareTo​(PedPedigree ped)
        Specified by:
        compareTo in interface java.lang.Comparable<PedPedigree>

      • families

        public java.util.Collection<PedPedigree> families()
        Split data into families
        Returns:

      • get

        public TfamEntry get​(java.lang.String id)

      • getFamilyId

        public java.lang.String getFamilyId()

      • getPlinkMap

        public PlinkMap getPlinkMap()

      • getSampleIds

        public java.util.List<java.lang.String> getSampleIds()
        Get a list of sample IDs
        Returns:

      • iterator

        public java.util.Iterator<TfamEntry> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<TfamEntry>

      • keySet

        public java.util.Set<java.lang.String> keySet()

      • load

        public void load​(java.lang.String pedFileName)
        Load a pedigree from a PED and MAP file pair
        Parameters:
        pedFileName -

      • loadTfam

        public void loadTfam​(java.lang.String tfamFileName)
        Load a TFAM file
        Parameters:
        tfamFileName -

      • saveTfam

        public void saveTfam​(java.lang.String fileName)
        Save pedigree as a TFAM file
        Parameters:
        fileName -

      • setVerbose

        public void setVerbose​(boolean verbose)

      • size

        public int size()

      • toString

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

      • values

        public java.util.Collection<TfamEntry> values()