umcg.genetica.io.trityper

Class TriTyperGenotypeData

java.lang.Object

umcg.genetica.io.trityper.TriTyperGenotypeData

public class TriTyperGenotypeData
extends Object

Author:

harmjan

Constructor Summary

Constructors

Constructor and Description
TriTyperGenotypeData()
TriTyperGenotypeData(String loc)

Method Summary

Modifier and Type	Method and Description
SNPLoader	createSNPLoader()
Byte	getChr(int s)
int	getChrPos(int s)
String	getDosageFileName()
String	getGenotypeFileName()
Integer	getIndividualId(String key)
String[]	getIndividuals()
gnu.trove.map.hash.TObjectIntHashMap<String>	getIndividualToId()
Boolean[]	getIsCase()
Boolean[]	getIsFemale()
Boolean[]	getIsIncluded()
SNP	getSNPObject(int d)
String[]	getSNPs()
gnu.trove.map.hash.TObjectIntHashMap<String>	getSnpToSNPId()
void	load(String loc)
void	setDosageFileName(String dosageFileName)
void	setGenotypeFileName(String genotypeFileName)
void	setIndividualToId(gnu.trove.map.hash.TObjectIntHashMap<String> individualToId)
void	setIsCase(Boolean[] isCase)
void	setIsFemale(Boolean[] isFemale)
void	setIsIncluded(Boolean[] isIncluded)
void	setSNPs(String[] SNPs)
void	setSnpToSNPObject(gnu.trove.map.hash.TObjectIntHashMap<String> snpToSNPObject)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TriTyperGenotypeData

public TriTyperGenotypeData(String loc)
                     throws IOException

Throws:

IOException

TriTyperGenotypeData

public TriTyperGenotypeData()

Method Detail

load

public final void load(String loc)
                throws IOException

Throws:

IOException

getIsFemale

public Boolean[] getIsFemale()

Returns:

the isFemale

setIsFemale

public void setIsFemale(Boolean[] isFemale)

Parameters:

isFemale - the isFemale to set

getIsCase

public Boolean[] getIsCase()

Returns:

the isCase

setIsCase

public void setIsCase(Boolean[] isCase)

Parameters:

isCase - the isCase to set

getIsIncluded

public Boolean[] getIsIncluded()

Returns:

the isIncluded

setIsIncluded

public void setIsIncluded(Boolean[] isIncluded)

Parameters:

isIncluded - the isIncluded to set

getIndividualToId

public gnu.trove.map.hash.TObjectIntHashMap<String> getIndividualToId()

Returns:

the individualToId

setIndividualToId

public void setIndividualToId(gnu.trove.map.hash.TObjectIntHashMap<String> individualToId)

Parameters:

individualToId - the individualToId to set

getSnpToSNPId

public gnu.trove.map.hash.TObjectIntHashMap<String> getSnpToSNPId()

Returns:

the snpToSNPObject

setSnpToSNPObject

public void setSnpToSNPObject(gnu.trove.map.hash.TObjectIntHashMap<String> snpToSNPObject)

Parameters:

snpToSNPObject - the snpToSNPObject to set

getGenotypeFileName

public String getGenotypeFileName()

Returns:

the genotypeFileName

setGenotypeFileName

public void setGenotypeFileName(String genotypeFileName)

Parameters:

genotypeFileName - the genotypeFileName to set

getDosageFileName

public String getDosageFileName()

Returns:

the dosageFileName

setDosageFileName

public void setDosageFileName(String dosageFileName)

Parameters:

dosageFileName - the dosageFileName to set

getSNPs

public String[] getSNPs()

Returns:

the SNPs

setSNPs

public void setSNPs(String[] SNPs)

Parameters:

SNPs - the SNPs to set

getIndividuals

public String[] getIndividuals()

getIndividualId

public Integer getIndividualId(String key)

getChr

public Byte getChr(int s)

getChrPos

public int getChrPos(int s)

getSNPObject

public SNP getSNPObject(int d)

createSNPLoader

public SNPLoader createSNPLoader()
                          throws IOException

Throws:

IOException