Class TfamEntry

java.lang.Object
org.snpeff.ped.TfamEntry
All Implemented Interfaces:
Comparable<TfamEntry>
Direct Known Subclasses:
PedEntry

public class TfamEntry extends Object implements Comparable<TfamEntry>
An entry in a TFAM table. I.e. a line in a PLINK's TFAM file
Author:
pcingola
  • Field Details

    • 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:
    • PHENOTYPE_CONTROL

      public static final int PHENOTYPE_CONTROL
      See Also:
    • PHENOTYPE_MISSING

      public static final int PHENOTYPE_MISSING
      See Also:
  • Constructor Details

    • TfamEntry

      public TfamEntry(String line)
    • TfamEntry

      public TfamEntry(String familyId, String id, String fatherId, String motherId, Sex sex, double phenotype)
  • Method Details

    • compareTo

      public int compareTo(TfamEntry ind)
      Specified by:
      compareTo in interface Comparable<TfamEntry>
    • getFamilyId

      public String getFamilyId()
    • getFatherId

      public String getFatherId()
    • getId

      public String getId()
    • getMotherId

      public 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(String line)
      Parse a line form a TFAM file
      Parameters:
      line -
    • parse

      protected int parse(String[] fields)
      Parse fields form a line
      Parameters:
      fields -
    • toString

      public String toString()
      Overrides:
      toString in class Object