alun.linkage
Class LinkagePedigreeData

java.lang.Object
  alun.linkage.LinkagePedigreeData

All Implemented Interfaces:

LinkConstants

public class LinkagePedigreeData
extends java.lang.Object
implements LinkConstants

A structure representing the data from a linkage .ped file.

Field Summary

boolean

twosexes

Fields inherited from interface alun.linkage.LinkConstants

FEMALE, MALE, PREMAKE, STANDARD, TRIPLET

Constructor Summary

LinkagePedigreeData()

LinkagePedigreeData(java.util.Collection<LinkageIndividual> v)

LinkagePedigreeData(LinkageFormatter b, LinkageParameterData par)

LinkagePedigreeData(LinkageFormatter b, LinkageParameterData par, boolean premake)

LinkagePedigreeData(LinkageFormatter b, LinkageParameterData par, int format)

LinkagePedigreeData(LinkagePedigreeData p, int[] x)

Method Summary

int	firstPedid()
LinkageIndividual[]	getIndividuals() Returns the array of individual data structures.
Pedigree	getPedigree() Creates a checked Pedigree structure from the list of individuals.
LinkageIndividual	ma(LinkageIndividual x)
static void	main(java.lang.String[] args) Main reads in a linkage parameter file and a linkage pedigree file which is in short form and output the linkage pedigree file in long form.
int	nIndividuals()
LinkageIndividual	pa(LinkageIndividual x)
void	set(java.util.Collection<LinkageIndividual> v)
LinkagePedigreeData[]	splitByPedigree()
java.lang.String	toString() Returns a string representing the data for the given pedigrees in the same format as it was read in from the linkage .ped file.
void	writeTo(java.io.PrintStream s)
void	writeTo(java.io.PrintWriter p)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

twosexes

public boolean twosexes

Constructor Detail

LinkagePedigreeData

public LinkagePedigreeData()

LinkagePedigreeData

public LinkagePedigreeData(LinkageFormatter b,
                           LinkageParameterData par,
                           int format)
                    throws java.io.IOException

Throws:

java.io.IOException

LinkagePedigreeData

public LinkagePedigreeData(LinkageFormatter b,
                           LinkageParameterData par,
                           boolean premake)
                    throws java.io.IOException

Throws:

java.io.IOException

LinkagePedigreeData

public LinkagePedigreeData(LinkageFormatter b,
                           LinkageParameterData par)
                    throws java.io.IOException

Throws:

java.io.IOException

LinkagePedigreeData

public LinkagePedigreeData(LinkagePedigreeData p,
                           int[] x)

LinkagePedigreeData

public LinkagePedigreeData(java.util.Collection<LinkageIndividual> v)

Method Detail

set

public void set(java.util.Collection<LinkageIndividual> v)

pa

public LinkageIndividual pa(LinkageIndividual x)

ma

public LinkageIndividual ma(LinkageIndividual x)

getIndividuals

public LinkageIndividual[] getIndividuals()

Returns the array of individual data structures.

nIndividuals

public int nIndividuals()

firstPedid

public int firstPedid()

toString

public java.lang.String toString()

Returns a string representing the data for the given pedigrees in the same format as it was read in from the linkage .ped file.

Overrides:

toString in class java.lang.Object

writeTo

public void writeTo(java.io.PrintStream s)

writeTo

public void writeTo(java.io.PrintWriter p)

getPedigree

public Pedigree getPedigree()

Creates a checked Pedigree structure from the list of individuals.

splitByPedigree

public LinkagePedigreeData[] splitByPedigree()

main

public static void main(java.lang.String[] args)

Main reads in a linkage parameter file and a linkage pedigree file which is in short form and output the linkage pedigree file in long form.