Package org.snpeff.ped

Class TfamEntry

java.lang.Object

org.snpeff.ped.TfamEntry

All Implemented Interfaces:

java.lang.Comparable<TfamEntry>

Direct Known Subclasses:

PedEntry

public class TfamEntry
extends java.lang.Object
implements java.lang.Comparable<TfamEntry>

An entry in a TFAM table. I.e. a line in a PLINK's TFAM file

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static int	PHENOTYPE_CASE	From PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affected
static int	PHENOTYPE_CONTROL
static int	PHENOTYPE_MISSING

Constructor Summary

Constructors

Constructor	Description
TfamEntry(java.lang.String line)
TfamEntry(java.lang.String familyId, java.lang.String id, java.lang.String fatherId, java.lang.String motherId, Sex sex, double phenotype)

Method Summary

Modifier and Type	Method	Description
int	compareTo(TfamEntry ind)
java.lang.String	getFamilyId()
java.lang.String	getFatherId()
java.lang.String	getId()
java.lang.String	getMotherId()
double	getPhenotype()
Sex	getSex()
boolean	isCase()	Is phenotype 'Case'?
boolean	isControl()	Is phenotype 'Control'?
boolean	isMissing()	Is phenotype 'Missing'?
protected void	parse(java.lang.String line)	Parse a line form a TFAM file
protected int	parse(java.lang.String[] fields)	Parse fields form a line
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

PHENOTYPE_CASE

public static final int PHENOTYPE_CASE

From PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affected

See Also:

Constant Field Values

PHENOTYPE_CONTROL

public static final int PHENOTYPE_CONTROL

See Also:

Constant Field Values

PHENOTYPE_MISSING

public static final int PHENOTYPE_MISSING

See Also:

Constant Field Values

Constructor Detail

TfamEntry

public TfamEntry(java.lang.String line)

TfamEntry

public TfamEntry(java.lang.String familyId,
                 java.lang.String id,
                 java.lang.String fatherId,
                 java.lang.String motherId,
                 Sex sex,
                 double phenotype)

Method Detail

compareTo

public int compareTo(TfamEntry ind)

Specified by:

compareTo in interface java.lang.Comparable<TfamEntry>

getFamilyId

public java.lang.String getFamilyId()

getFatherId

public java.lang.String getFatherId()

getId

public java.lang.String getId()

getMotherId

public java.lang.String getMotherId()

getPhenotype

public double getPhenotype()

getSex

public Sex getSex()

isCase

public boolean isCase()

Is phenotype 'Case'?

Returns:

isControl

public boolean isControl()

Is phenotype 'Control'?

Returns:

isMissing

public boolean isMissing()

Is phenotype 'Missing'?

Returns:

parse

protected void parse(java.lang.String line)

Parse a line form a TFAM file

Parameters:

line -

parse

protected int parse(java.lang.String[] fields)

Parse fields form a line

Parameters:

fields -

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object