Class PedPedigree

java.lang.Object
org.snpeff.ped.PedPedigree
All Implemented Interfaces:
Comparable<PedPedigree>, Iterable<TfamEntry>
Direct Known Subclasses:
PedFamily

public class PedPedigree extends Object implements Iterable<TfamEntry>, Comparable<PedPedigree>
A pedigree of PedEntries
Author:
pcingola
  • Constructor Details

    • PedPedigree

      public PedPedigree()
    • PedPedigree

      public PedPedigree(String tfamFileName)
  • Method Details

    • 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 Comparable<PedPedigree>
    • families

      public Collection<PedPedigree> families()
      Split data into families
      Returns:
    • get

      public TfamEntry get(String id)
    • getFamilyId

      public String getFamilyId()
    • getPlinkMap

      public PlinkMap getPlinkMap()
    • getSampleIds

      public List<String> getSampleIds()
      Get a list of sample IDs
      Returns:
    • iterator

      public Iterator<TfamEntry> iterator()
      Specified by:
      iterator in interface Iterable<TfamEntry>
    • keySet

      public Set<String> keySet()
    • load

      public void load(String pedFileName)
      Load a pedigree from a PED and MAP file pair
      Parameters:
      pedFileName -
    • loadTfam

      public void loadTfam(String tfamFileName)
      Load a TFAM file
      Parameters:
      tfamFileName -
    • saveTfam

      public void saveTfam(String fileName)
      Save pedigree as a TFAM file
      Parameters:
      fileName -
    • setVerbose

      public void setVerbose(boolean verbose)
    • size

      public int size()
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • values

      public Collection<TfamEntry> values()