java.lang.Object
- main.Pedigree

```
public class Pedigree
extends java.lang.Object
```
Class Pedigree stores parent-offspring relationships in a list of samples. In particular, class Pedigree stores a list of the single individuals in the list of samples, a list of the parent-offspring duos in the list of samples, and a list of the parent-offspring trios in the list of samples. A single individual is an individuals without a parent or offspring in the list of samples.

Instances of class Pedigree are immutable.

Constructor Summary

Constructors
Constructor Description

Pedigree(Samples samples, java.io.File pedFile)
Constructs a new NuclearFamilies instance.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`duoOffspring(int index)`	Returns the sample index of the offspring of the specified parent-offspring duo.
`int`	`duoParent(int index)`	Returns the sample index of the parent of the specified parent-offspring duo.
`int`	`father(int sample)`	Returns the sample index of the father of the specified sample, or returns `-1` if the father is unknown or is not present in the list of samples.
`int`	`mother(int sample)`	Returns the sample index of the mother of the specified sample, or returns `-1` if the mother is unknown or is not present in the list of samples.
`int`	`nDuos()`	Returns the number of parent-offspring duos in the list of samples.
`int`	`nOffspring(int sample)`	Returns the number of offspring of the specified sample.
`int`	`nSamples()`	Returns the number of samples.
`int`	`nSingles()`	Returns the number of single individuals in the list of samples.
`int`	`nTrios()`	Returns the number of parent-offspring trios in the list of samples.
`int`	`offspring(int sample, int index)`	Returns the sample index of the offspring of the specified sample.
`int[]`	`relateds()`	Returns an array of indices of samples with at least one parent or child in the list or samples.
`Samples`	`samples()`	Returns the list of samples.
`int`	`single(int index)`	Returns the sample index of the specified single individual.
`int[]`	`singles()`	Returns an array of indices of samples with no parents or children in the list of samples.
`java.lang.String`	`toString()`	Returns a string representation of `this`.
`int`	`trioFather(int index)`	Returns the sample index of the father of the specified parent-offspring trio.
`int`	`trioMother(int index)`	Returns the sample index of the mother of the specified parent-offspring trio.
`int`	`trioOffspring(int index)`	Returns the sample index of the offspring of the specified parent-offspring trio.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Pedigree
```
public Pedigree(Samples samples,
                java.io.File pedFile)
```
    Constructs a new NuclearFamilies instance.
    
    Parameters:
    
    samples - the list of samples.
    
    pedFile - a linkage-format pedigree file, or null if no pedigree relationships are known. A pedigree file must have at least 4 white-space delimited columns. The first column of the pedigree file (family ID) is ignored. The second, third, and fourth columns are the individual's ID, the individual's father's ID, and the individual's mother's ID respectively.
    
    Throws:
    
    java.lang.IllegalArgumentException - if a pedigree file is specified, and if the file has a non-blank line with less than 4 white-space delimited fields
    
    java.lang.IllegalArgumentException - if a pedigree file is specified, and if the file has duplicate individual identifiers in the second white-space delimited column
    
    java.lang.NullPointerException - if samples == null
- Method Detail
  - samples
```
public Samples samples()
```
    Returns the list of samples.
    
    Returns:
    
    the list of samples
  - nSamples
```
public int nSamples()
```
    Returns the number of samples.
    
    Returns:
    
    the number of samples
  - nSingles
```
public int nSingles()
```
    Returns the number of single individuals in the list of samples. A single individual has no parent or offspring in the list of samples.
    
    Returns:
    
    the number of single individuals in the sample
  - nDuos
```
public int nDuos()
```
    Returns the number of parent-offspring duos in the list of samples. The offspring of a parent-offspring duo has only one parent in the sample.
    
    Returns:
    
    the number of parent-offspring duos in the list of samples
  - nTrios
```
public int nTrios()
```
    Returns the number of parent-offspring trios in the list of samples. The offspring of a parent-offspring trio has two parents in the sample.
    
    Returns:
    
    the number of parent-offspring trios in the list of samples
  - singles
```
public int[] singles()
```
    Returns an array of indices of samples with no parents or children in the list of samples.
    
    Returns:
    
    an array of indices of samples with no parents or children in the list of samples
  - relateds
```
public int[] relateds()
```
    Returns an array of indices of samples with at least one parent or child in the list or samples.
    
    Returns:
    
    an array of indices of samples with at least one parent or child in the list or samples
  - single
```
public int single(int index)
```
    Returns the sample index of the specified single individual. A single individual has no first-degree relative in the list of samples.
    
    Parameters:
    
    index - the index of a single individual
    
    Returns:
    
    the sample index of the specified single individual
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nSingles()
  - duoParent
```
public int duoParent(int index)
```
    Returns the sample index of the parent of the specified parent-offspring duo.
    
    Parameters:
    
    index - the index of a parent-offspring duo
    
    Returns:
    
    the sample index of the parent of the specified parent-offspring duo
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nDuos()
  - duoOffspring
```
public int duoOffspring(int index)
```
    Returns the sample index of the offspring of the specified parent-offspring duo.
    
    Parameters:
    
    index - the index of a parent-offspring duo
    
    Returns:
    
    the sample index of the offspring of the specified parent-offspring duo
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nDuos()
  - trioFather
```
public int trioFather(int index)
```
    Returns the sample index of the father of the specified parent-offspring trio.
    
    Parameters:
    
    index - the index of a parent-offspring trio
    
    Returns:
    
    the sample index of the father of the specified parent-offspring trio
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nTrios()
  - trioMother
```
public int trioMother(int index)
```
    Returns the sample index of the mother of the specified parent-offspring trio.
    
    Parameters:
    
    index - the index of a parent-offspring trio
    
    Returns:
    
    the sample index of the mother of the specified parent-offspring trio
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nTrios()
  - trioOffspring
```
public int trioOffspring(int index)
```
    Returns the sample index of the offspring of the specified parent-offspring trio.
    
    Parameters:
    
    index - the index of a parent-offspring trio
    
    Returns:
    
    the sample index of the offspring of the specified parent-offspring trio
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nTrios()
  - father
```
public int father(int sample)
```
    Returns the sample index of the father of the specified sample, or returns -1 if the father is unknown or is not present in the list of samples.
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    the sample index of the father of the specified sample, or -1 if the father is unknown or is not present in the list of samples
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.size()()
  - mother
```
public int mother(int sample)
```
    Returns the sample index of the mother of the specified sample, or returns -1 if the mother is unknown or is not present in the list of samples.
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    the sample index of the mother of the specified sample, or -1 if the mother is unknown or is not present in the list of samples
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.size()()
  - nOffspring
```
public int nOffspring(int sample)
```
    Returns the number of offspring of the specified sample.
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    the number of offspring of the specified sample
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.size()()
  - offspring
```
public int offspring(int sample,
                     int index)
```
    Returns the sample index of the offspring of the specified sample.
    
    Parameters:
    
    sample - a sample index
    
    index - the offspring index
    
    Returns:
    
    the sample index of the offspring of the specified sample.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.size()()
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nOffspring(sample)
  - toString
```
public java.lang.String toString()
```
    Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string representation of this

Class Pedigree

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Pedigree

Method Detail

samples

nSamples

nSingles

nDuos

nTrios

singles

relateds

single

duoParent

duoOffspring

trioFather

trioMother

trioOffspring

father

mother

nOffspring

offspring

toString