Package org.snpeff.ped
Class PedPedigree
- java.lang.Object
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- org.snpeff.ped.PedPedigree
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- All Implemented Interfaces:
java.lang.Comparable<PedPedigree>
,java.lang.Iterable<TfamEntry>
- Direct Known Subclasses:
PedFamily
public class PedPedigree extends java.lang.Object implements java.lang.Iterable<TfamEntry>, java.lang.Comparable<PedPedigree>
A pedigree of PedEntries- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description PedPedigree()
PedPedigree(java.lang.String tfamFileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(TfamEntry tfamEntry)
Add an entry to this pedigreeint
compareTo(PedPedigree ped)
java.util.Collection<PedPedigree>
families()
Split data into familiesTfamEntry
get(java.lang.String id)
java.lang.String
getFamilyId()
PlinkMap
getPlinkMap()
java.util.List<java.lang.String>
getSampleIds()
Get a list of sample IDsjava.util.Iterator<TfamEntry>
iterator()
java.util.Set<java.lang.String>
keySet()
void
load(java.lang.String pedFileName)
Load a pedigree from a PED and MAP file pairvoid
loadTfam(java.lang.String tfamFileName)
Load a TFAM filevoid
saveTfam(java.lang.String fileName)
Save pedigree as a TFAM filevoid
setVerbose(boolean verbose)
int
size()
java.lang.String
toString()
java.util.Collection<TfamEntry>
values()
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Method Detail
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add
public void add(TfamEntry tfamEntry)
Add an entry to this pedigree- Parameters:
tfamEntry
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compareTo
public int compareTo(PedPedigree ped)
- Specified by:
compareTo
in interfacejava.lang.Comparable<PedPedigree>
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families
public java.util.Collection<PedPedigree> families()
Split data into families- Returns:
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get
public TfamEntry get(java.lang.String id)
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getFamilyId
public java.lang.String getFamilyId()
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getPlinkMap
public PlinkMap getPlinkMap()
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getSampleIds
public java.util.List<java.lang.String> getSampleIds()
Get a list of sample IDs- Returns:
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iterator
public java.util.Iterator<TfamEntry> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<TfamEntry>
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keySet
public java.util.Set<java.lang.String> keySet()
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load
public void load(java.lang.String pedFileName)
Load a pedigree from a PED and MAP file pair- Parameters:
pedFileName
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loadTfam
public void loadTfam(java.lang.String tfamFileName)
Load a TFAM file- Parameters:
tfamFileName
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saveTfam
public void saveTfam(java.lang.String fileName)
Save pedigree as a TFAM file- Parameters:
fileName
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setVerbose
public void setVerbose(boolean verbose)
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size
public int size()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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values
public java.util.Collection<TfamEntry> values()
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