umcg.genetica.io.trityper

Class SNPLoader

java.lang.Object

umcg.genetica.io.trityper.SNPLoader

public class SNPLoader
extends Object

Author:

harm-jan

Constructor Summary

Constructors

Constructor and Description
SNPLoader(RandomAccessFile genotypehandle, Boolean[] indIsIncluded, Boolean[] isFemale)
SNPLoader(RandomAccessFile genotypehandle, RandomAccessFile dosagehandle, Boolean[] indIsIncluded, Boolean[] isFemale)

Method Summary

Modifier and Type	Method and Description
void	close()
double	getAverageSNPSize(int numSNPs)
int	getNumIndividuals()
boolean	hasDosageInformation()
void	loadDosage(SNP snp)
void	loadGenotypes(SNP snp)
void	setNumIndividuals(int numIndividuals)

Methods inherited from class java.lang.Object

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

Constructor Detail

SNPLoader

public SNPLoader(RandomAccessFile genotypehandle,
                 Boolean[] indIsIncluded,
                 Boolean[] isFemale)

SNPLoader

public SNPLoader(RandomAccessFile genotypehandle,
                 RandomAccessFile dosagehandle,
                 Boolean[] indIsIncluded,
                 Boolean[] isFemale)

Method Detail

loadGenotypes

public void loadGenotypes(SNP snp)
                   throws IOException

Throws:

IOException

loadDosage

public void loadDosage(SNP snp)
                throws IOException

Throws:

IOException

getNumIndividuals

public int getNumIndividuals()

Returns:

the numIndividuals

setNumIndividuals

public void setNumIndividuals(int numIndividuals)

Parameters:

numIndividuals - the numIndividuals to set

hasDosageInformation

public boolean hasDosageInformation()

getAverageSNPSize

public double getAverageSNPSize(int numSNPs)
                         throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Throws:

IOException