alun.genio
Class LinkageIndividual

java.lang.Object
  alun.genio.LinkageIndividual

public class LinkageIndividual
extends java.lang.Object

A class that contains the information for an individual from the linkage .ped file.

Field Summary

java.lang.String	comment A string representing anything that was left on this individual's input line after all thee pedigree, sex, proband and locus informatio was read in.
int	firstbornid The individual's first born child's id number.
int	id The individual's id number.
int	index
int	maid The individual's mother's id number.
int	masnextid The individual's mother's next born child's id number.
int	paid The individual's father's id number.
int	pasnextid The individual's father's next born child's id number.
int	pedid The individual's pedigree id number.
LinkagePhenotype[]	pheno A list of phenotypes as read in from the input line.
static int	PREMAKE
int	proband The individual's proband status coded as 1 for proband 0 for non-proband.
int	sex The individual's sex coded as 1 for male and 2 for female.
static int	STANDARD
static int	TRIPLET

Constructor Summary

LinkageIndividual()

LinkageIndividual(LinkageFormatter b, LinkageParameterData par, boolean premake)
Creates a new linkage individual by reading the data from the given input formatter.

LinkageIndividual(LinkageFormatter b, LinkageParameterData par, int format)

LinkageIndividual(LinkageIndividual l, int[] x)

Method Summary

LinkagePhenotype	getPhenotype(int i)
LinkagePhenotype[]	getPhenotypes() Returns the array of linkage phonetypes for this individual.
java.lang.String	longString() Returns a string representation of this individual's data in the same format as the original linkage input .ped file.
java.lang.String	shortString() Returns a string representation of this individual's data in pre makeped format.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

STANDARD

public static final int STANDARD

See Also:

Constant Field Values

PREMAKE

public static final int PREMAKE

See Also:

Constant Field Values

TRIPLET

public static final int TRIPLET

See Also:

Constant Field Values

index

public int index

pedid

public int pedid

The individual's pedigree id number.

id

public int id

The individual's id number.

paid

public int paid

The individual's father's id number.

maid

public int maid

The individual's mother's id number.

firstbornid

public int firstbornid

The individual's first born child's id number.

pasnextid

public int pasnextid

The individual's father's next born child's id number.

masnextid

public int masnextid

The individual's mother's next born child's id number.

sex

public int sex

The individual's sex coded as 1 for male and 2 for female.

proband

public int proband

The individual's proband status coded as 1 for proband 0 for non-proband.

comment

public java.lang.String comment

A string representing anything that was left on this individual's input line after all thee pedigree, sex, proband and locus informatio was read in.

pheno

public LinkagePhenotype[] pheno

A list of phenotypes as read in from the input line. For co-dominant markers these phenotypes will be the genotypes.

Constructor Detail

LinkageIndividual

public LinkageIndividual()

LinkageIndividual

public LinkageIndividual(LinkageIndividual l,
                         int[] x)

LinkageIndividual

public LinkageIndividual(LinkageFormatter b,
                         LinkageParameterData par,
                         boolean premake)

Creates a new linkage individual by reading the data from the given input formatter. Checks the data for consiency with with the data from the parameter file as specified in the second argument.

LinkageIndividual

public LinkageIndividual(LinkageFormatter b,
                         LinkageParameterData par,
                         int format)

Method Detail

getPhenotypes

public LinkagePhenotype[] getPhenotypes()

Returns the array of linkage phonetypes for this individual.

getPhenotype

public LinkagePhenotype getPhenotype(int i)

longString

public java.lang.String longString()

Returns a string representation of this individual's data in the same format as the original linkage input .ped file.

shortString

public java.lang.String shortString()

Returns a string representation of this individual's data in pre makeped format.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object