Package org.snpeff.ped

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()