Package org.snpeff.ped
Class TfamEntry
- java.lang.Object
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- org.snpeff.ped.TfamEntry
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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 affectedstatic int
PHENOTYPE_CONTROL
static int
PHENOTYPE_MISSING
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Method Summary
All Methods Instance Methods Concrete Methods 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 fileprotected int
parse(java.lang.String[] fields)
Parse fields form a linejava.lang.String
toString()
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Field Detail
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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
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PHENOTYPE_CONTROL
public static final int PHENOTYPE_CONTROL
- See Also:
- Constant Field Values
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PHENOTYPE_MISSING
public static final int PHENOTYPE_MISSING
- See Also:
- Constant Field Values
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Constructor Detail
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TfamEntry
public TfamEntry(java.lang.String line)
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TfamEntry
public TfamEntry(java.lang.String familyId, java.lang.String id, java.lang.String fatherId, java.lang.String motherId, Sex sex, double phenotype)
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Method Detail
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compareTo
public int compareTo(TfamEntry ind)
- Specified by:
compareTo
in interfacejava.lang.Comparable<TfamEntry>
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getFamilyId
public java.lang.String getFamilyId()
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getFatherId
public java.lang.String getFatherId()
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getId
public java.lang.String getId()
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getMotherId
public java.lang.String getMotherId()
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getPhenotype
public double getPhenotype()
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getSex
public Sex getSex()
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isCase
public boolean isCase()
Is phenotype 'Case'?- Returns:
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isControl
public boolean isControl()
Is phenotype 'Control'?- Returns:
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isMissing
public boolean isMissing()
Is phenotype 'Missing'?- Returns:
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parse
protected void parse(java.lang.String line)
Parse a line form a TFAM file- Parameters:
line
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parse
protected int parse(java.lang.String[] fields)
Parse fields form a line- Parameters:
fields
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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