Package org.snpeff.ped
Class TfamEntry
java.lang.Object
org.snpeff.ped.TfamEntry
- All Implemented Interfaces:
Comparable<TfamEntry>
- Direct Known Subclasses:
PedEntry
An entry in a TFAM table.
I.e. a line in a PLINK's TFAM file
- Author:
- pcingola
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
From PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affectedstatic final int
static final int
-
Constructor Summary
Constructors -
Method Summary
-
Field Details
-
PHENOTYPE_CASE
public static final int PHENOTYPE_CASEFrom PLINK's manual: Affection status, by default, should be coded: -9 missing 0 missing 1 unaffected 2 affected- See Also:
-
PHENOTYPE_CONTROL
public static final int PHENOTYPE_CONTROL- See Also:
-
PHENOTYPE_MISSING
public static final int PHENOTYPE_MISSING- See Also:
-
-
Constructor Details
-
TfamEntry
-
TfamEntry
-
-
Method Details
-
compareTo
- Specified by:
compareTo
in interfaceComparable<TfamEntry>
-
getFamilyId
-
getFatherId
-
getId
-
getMotherId
-
getPhenotype
public double getPhenotype() -
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
Parse a line form a TFAM file- Parameters:
line
-
-
parse
Parse fields form a line- Parameters:
fields
-
-
toString
-