umcg.genetica.io.binInteraction

Class BinaryInteractionFile

java.lang.Object

umcg.genetica.io.binInteraction.BinaryInteractionFile

All Implemented Interfaces:

Closeable, AutoCloseable

public class BinaryInteractionFile
extends Object
implements Closeable

Author:

Patrick Deelen

Field Summary

Fields

Modifier and Type	Field and Description
protected String[]	covariates
protected static byte	MAGIC_1
protected static byte	MAGIC_2
protected long	sizeInteractionBlock

Constructor Summary

Constructors

Modifier

Constructor and Description

protected

BinaryInteractionFile(File interactionFile, boolean readOnly, BinaryInteractionCohort[] cohorts, BinaryInteractionGene[] genes, BinaryInteractionVariant[] variants, String[] covariates, int[][] covariatesTested, long timeStamp, boolean allCovariants, boolean metaAnalysis, boolean normalQtlStored, boolean flippedZscoreStored, String fileDescription, long interactions, long startQtlBlock, long startInteractionBlock)

Method Summary

Modifier and Type	Method and Description
boolean	areAllCovariatesTestedForAllVariantGenes()
protected static long	calculateSizeInteractionResultBlock(int cohorts, boolean flippedZscoreStored, boolean metaAnalysis)
protected static long	calculateSizeNormalQtlBlock(int cohorts, boolean metaAnalysis)
void	close()
boolean	containsCovariant(String covariateName)
boolean	containsGene(String geneName)
boolean	containsInteraction(String variantName, String geneName, String covariateName)
boolean	containsVariant(String variantName)
boolean	containsVariantGene(String variantName, String geneName)
void	finalizeWriting()
int	getCohortCount()
List<BinaryInteractionCohort>	getCohorts()
int	getCovariateCount()
List<String>	getCovariates()
long	getCreationDataEpoch()
String	getCreationDataTimeString()
String	getFileDescription()
BinaryInteractionGene	getGene(int pointer)
BinaryInteractionGene	getGene(String name)
int	getGeneCount()
List<BinaryInteractionGene>	getGenes()
File	getInteractionFile()
long	getInteractionReadBufferLoaded()
long	getInteractionWriteBufferFlushed()
long	getInteractionZscoresRead()
long	getInteractionZscoresSet()
long	getQtlReadBufferLoaded()
long	getQtlWriteBufferFlushed()
long	getQtlZscoresRead()
long	getQtlZscoresSet()
long	getTotalNumberInteractions()
BinaryInteractionVariant	getVariant(int pointer)
BinaryInteractionVariant	getVariant(String name)
BinaryInteractionVariant	getVariant(String chr, int pos)
int	getVariantCount()
int	getVariantGeneCombinations()
List<BinaryInteractionVariant>	getVariants()
boolean	isFlippedZscoreStored()
boolean	isMetaAnalysis()
boolean	isNormalQtlStored()
boolean	isReadOnly()
static BinaryInteractionFile	load(File interactionFile)
static BinaryInteractionFile	load(File interactionFile, boolean readOnly)
protected BinaryInteractionZscores	readInteractionResults(long interactionPointer)
BinaryInteractionZscores	readInteractionResults(String variantName, String geneName, String covariateName)
BinaryInteractionQtlZscores	readQtlResults(String variantName, String geneName)
BinaryInteractionQueryResult	readVariantGeneCovariateResults(String variantName, String geneName, String covariateName)
Iterator<BinaryInteractionQueryResult>	readVariantGeneResults(String variantName, String geneName)
void	setInteractionResults(String variantName, String geneName, String covariateName, BinaryInteractionZscores zscores)
void	setQtlResults(String variantName, String geneName, BinaryInteractionQtlZscores zscores)

Methods inherited from class java.lang.Object

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

Field Detail

MAGIC_1

protected static final byte MAGIC_1

See Also:

Constant Field Values

MAGIC_2

protected static final byte MAGIC_2

See Also:

Constant Field Values

covariates

protected final String[] covariates

sizeInteractionBlock

protected final long sizeInteractionBlock

Constructor Detail

BinaryInteractionFile

protected BinaryInteractionFile(File interactionFile,
                                boolean readOnly,
                                BinaryInteractionCohort[] cohorts,
                                BinaryInteractionGene[] genes,
                                BinaryInteractionVariant[] variants,
                                String[] covariates,
                                int[][] covariatesTested,
                                long timeStamp,
                                boolean allCovariants,
                                boolean metaAnalysis,
                                boolean normalQtlStored,
                                boolean flippedZscoreStored,
                                String fileDescription,
                                long interactions,
                                long startQtlBlock,
                                long startInteractionBlock)
                         throws BinaryInteractionFileException,
                                FileNotFoundException,
                                IOException

Throws:

BinaryInteractionFileException

FileNotFoundException

IOException

Method Detail

load

public static BinaryInteractionFile load(File interactionFile)
                                  throws FileNotFoundException,
                                         IOException,
                                         BinaryInteractionFileException

Throws:

FileNotFoundException

IOException

BinaryInteractionFileException

load

public static BinaryInteractionFile load(File interactionFile,
                                         boolean readOnly)
                                  throws FileNotFoundException,
                                         IOException,
                                         BinaryInteractionFileException

Throws:

FileNotFoundException

IOException

BinaryInteractionFileException

calculateSizeNormalQtlBlock

protected static long calculateSizeNormalQtlBlock(int cohorts,
                                                  boolean metaAnalysis)

calculateSizeInteractionResultBlock

protected static long calculateSizeInteractionResultBlock(int cohorts,
                                                          boolean flippedZscoreStored,
                                                          boolean metaAnalysis)

getInteractionFile

public File getInteractionFile()

isReadOnly

public boolean isReadOnly()

getCreationDataEpoch

public long getCreationDataEpoch()

getCreationDataTimeString

public String getCreationDataTimeString()

isMetaAnalysis

public boolean isMetaAnalysis()

isNormalQtlStored

public boolean isNormalQtlStored()

isFlippedZscoreStored

public boolean isFlippedZscoreStored()

getFileDescription

public String getFileDescription()

areAllCovariatesTestedForAllVariantGenes

public boolean areAllCovariatesTestedForAllVariantGenes()

getTotalNumberInteractions

public long getTotalNumberInteractions()

getCohorts

public List<BinaryInteractionCohort> getCohorts()

getGenes

public List<BinaryInteractionGene> getGenes()

getGene

public BinaryInteractionGene getGene(String name)
                              throws BinaryInteractionFileException

Throws:

BinaryInteractionFileException

getGene

public BinaryInteractionGene getGene(int pointer)
                              throws BinaryInteractionFileException

Throws:

BinaryInteractionFileException

getVariants

public List<BinaryInteractionVariant> getVariants()

getVariant

public BinaryInteractionVariant getVariant(String name)
                                    throws BinaryInteractionFileException

Throws:

BinaryInteractionFileException

getVariant

public BinaryInteractionVariant getVariant(int pointer)
                                    throws BinaryInteractionFileException

Throws:

BinaryInteractionFileException

getCovariates

public List<String> getCovariates()

finalizeWriting

public void finalizeWriting()
                     throws IOException,
                            BinaryInteractionFileException

Throws:

IOException

BinaryInteractionFileException

getQtlZscoresSet

public long getQtlZscoresSet()

getInteractionZscoresSet

public long getInteractionZscoresSet()

getQtlZscoresRead

public long getQtlZscoresRead()

getInteractionZscoresRead

public long getInteractionZscoresRead()

getInteractionWriteBufferFlushed

public long getInteractionWriteBufferFlushed()

getQtlWriteBufferFlushed

public long getQtlWriteBufferFlushed()

getInteractionReadBufferLoaded

public long getInteractionReadBufferLoaded()

getQtlReadBufferLoaded

public long getQtlReadBufferLoaded()

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException

readQtlResults

public BinaryInteractionQtlZscores readQtlResults(String variantName,
                                                  String geneName)
                                           throws BinaryInteractionFileException,
                                                  IOException

Throws:

BinaryInteractionFileException

IOException

setQtlResults

public void setQtlResults(String variantName,
                          String geneName,
                          BinaryInteractionQtlZscores zscores)
                   throws BinaryInteractionFileException,
                          IOException

Throws:

BinaryInteractionFileException

IOException

readInteractionResults

public BinaryInteractionZscores readInteractionResults(String variantName,
                                                       String geneName,
                                                       String covariateName)
                                                throws BinaryInteractionFileException,
                                                       IOException

Throws:

BinaryInteractionFileException

IOException

readVariantGeneCovariateResults

public BinaryInteractionQueryResult readVariantGeneCovariateResults(String variantName,
                                                                    String geneName,
                                                                    String covariateName)
                                                             throws BinaryInteractionFileException,
                                                                    IOException

Throws:

BinaryInteractionFileException

IOException

readVariantGeneResults

public Iterator<BinaryInteractionQueryResult> readVariantGeneResults(String variantName,
                                                                     String geneName)
                                                              throws BinaryInteractionFileException,
                                                                     IOException

Throws:

BinaryInteractionFileException

IOException

readInteractionResults

protected BinaryInteractionZscores readInteractionResults(long interactionPointer)
                                                   throws BinaryInteractionFileException,
                                                          IOException

Throws:

BinaryInteractionFileException

IOException

setInteractionResults

public void setInteractionResults(String variantName,
                                  String geneName,
                                  String covariateName,
                                  BinaryInteractionZscores zscores)
                           throws BinaryInteractionFileException,
                                  IOException

Throws:

BinaryInteractionFileException

IOException

getGeneCount

public int getGeneCount()

getCovariateCount

public int getCovariateCount()

getVariantCount

public int getVariantCount()

getCohortCount

public int getCohortCount()

getVariantGeneCombinations

public int getVariantGeneCombinations()

containsGene

public boolean containsGene(String geneName)

containsVariant

public boolean containsVariant(String variantName)

containsCovariant

public boolean containsCovariant(String covariateName)

containsVariantGene

public boolean containsVariantGene(String variantName,
                                   String geneName)

containsInteraction

public boolean containsInteraction(String variantName,
                                   String geneName,
                                   String covariateName)
                            throws BinaryInteractionFileException

Throws:

BinaryInteractionFileException

getVariant

public BinaryInteractionVariant getVariant(String chr,
                                           int pos)

Parameters:

chr -

pos -

Returns:

null if not found