Package org.snpeff.ped
Class PedEntry
java.lang.Object
org.snpeff.ped.TfamEntry
org.snpeff.ped.PedEntry
- All Implemented Interfaces:
Comparable<TfamEntry>
,Iterable<PedGenotype>
An entry in a PED table.
I.e. a line in a PED file (PLINK)
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.ped.TfamEntry
PHENOTYPE_CASE, PHENOTYPE_CONTROL, PHENOTYPE_MISSING
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
Number of phenotypes availablegetGenotype
(int idx) Get genotype WARNING: Empty string means that no genotpye is availablegetGenotype
(String idStr) Get phenotype by String IDGet all genotype names WARNING: the returned string collection is unsorted!String[]
iterator()
protected void
Parse a line form a TFAM fileprotected int
Parse fields form a lineint
size()
Number of phenotypestoString()
Methods inherited from class org.snpeff.ped.TfamEntry
compareTo, getFamilyId, getFatherId, getId, getMotherId, getPhenotype, getSex, isCase, isControl, isMissing
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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PedEntry
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PedEntry
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Method Details
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countGenotypes
public int countGenotypes()Number of phenotypes available- Returns:
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getGenotype
Get genotype WARNING: Empty string means that no genotpye is available- Parameters:
idx
-- Returns:
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getGenotype
Get phenotype by String ID- Parameters:
idStr
-- Returns:
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getGenotypeNames
Get all genotype names WARNING: the returned string collection is unsorted!- Returns:
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getGenotypes
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iterator
- Specified by:
iterator
in interfaceIterable<PedGenotype>
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parse
Description copied from class:TfamEntry
Parse a line form a TFAM file -
parse
Description copied from class:TfamEntry
Parse fields form a line -
size
public int size()Number of phenotypes- Returns:
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toString
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