umcg.genetica.io.trityper

Class QTLTextFile

java.lang.Object

umcg.genetica.io.text.TextFile

umcg.genetica.io.trityper.QTLTextFile

All Implemented Interfaces:

Iterable<String>

public class QTLTextFile
extends TextFile

Author:

harmjan

Field Summary

Fields

Modifier and Type	Field and Description
static int	ASESSEDALLELE
static int	CISTRANS
static int	DATASECORR
static int	DATASETB
static int	DATASETNAMES
static int	DATASETSIZE
static int	DATASETZSCORE
static String	header
static int	HUGO
static int	METAB
static int	METAZ
static int	PROBE
static int	PROBECHR
static int	PROBELOC
static int	PVAL
static int	SNP
static int	SNPCHR
static int	SNPLOC
static int	SNPTYPE

Fields inherited from class umcg.genetica.io.text.TextFile

colon, comma, DEFAULT_BUFFER_SIZE, ENCODING, file, in, out, R, semicolon, space, tab, W, writeable

Constructor Summary

Constructors

Constructor and Description
QTLTextFile(String loc, boolean W)
QTLTextFile(String loc, boolean W, boolean gz)

Method Summary

Modifier and Type	Method and Description
Iterator<EQTL>	getEQtlIterator()
EQTL[]	read()
EQTL[]	readExpectedSize(int expSize)
ArrayList<EQTL>	readList()
void	write(ArrayList<EQTL> eqtllist)
void	write(EQTL[] eqtllist)

Methods inherited from class umcg.genetica.io.text.TextFile

append, append, close, countCols, countLines, flush, getFileName, iterator, open, readAsArray, readAsArray, readAsArrayList, readAsArrayList, readAsHashMap, readAsHashMap, readAsHashMap, readAsPairs, readAsSet, readAsTriple, readLine, readLineElems, readLineElemsIterable, readLineElemsReturnObjects, readLineElemsReturnReference, write, writeList, writeln, writeln, writeln, writelnDelimited, writelnsynced, writelnTabDelimited

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

PVAL

public static int PVAL

SNP

public static int SNP

SNPCHR

public static int SNPCHR

SNPLOC

public static int SNPLOC

PROBE

public static int PROBE

PROBECHR

public static int PROBECHR

PROBELOC

public static int PROBELOC

CISTRANS

public static int CISTRANS

SNPTYPE

public static int SNPTYPE

ASESSEDALLELE

public static int ASESSEDALLELE

METAZ

public static int METAZ

DATASETNAMES

public static int DATASETNAMES

DATASETZSCORE

public static int DATASETZSCORE

DATASETSIZE

public static int DATASETSIZE

HUGO

public static int HUGO

DATASECORR

public static int DATASECORR

METAB

public static int METAB

DATASETB

public static int DATASETB

header

public static String header

Constructor Detail

QTLTextFile

public QTLTextFile(String loc,
                   boolean W)
            throws IOException

Throws:

IOException

QTLTextFile

public QTLTextFile(String loc,
                   boolean W,
                   boolean gz)
            throws IOException

Throws:

IOException

Method Detail

write

public void write(EQTL[] eqtllist)
           throws IOException

Throws:

IOException

write

public void write(ArrayList<EQTL> eqtllist)
           throws IOException

Throws:

IOException

read

public EQTL[] read()
            throws IOException

Throws:

IOException

readList

public ArrayList<EQTL> readList()
                         throws IOException

Throws:

IOException

readExpectedSize

public EQTL[] readExpectedSize(int expSize)
                        throws IOException

Throws:

IOException

getEQtlIterator

public Iterator<EQTL> getEQtlIterator()
                               throws IOException

Throws:

IOException