Package org.snpeff.fileIterator

Class MarkerFileIterator<M extends Marker>

java.lang.Object

org.snpeff.fileIterator.FileIterator<M>

org.snpeff.fileIterator.MarkerFileIterator<M>

All Implemented Interfaces:

java.lang.Iterable<M>, java.util.Iterator<M>

Direct Known Subclasses:

GenericMarkerFileIterator, Gff3FileIterator, MotifFileIterator, RegulationFileIterator, VariantFileIterator, VcfFileIterator, VcfHapMapFileIterator

public abstract class MarkerFileIterator<M extends Marker>
extends FileIterator<M>

Opens a Marker file and iterates over all markers

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	createChromos
protected Genome	genome
protected boolean	ignoreChromosomeErrors
protected int	inOffset

Fields inherited from class org.snpeff.fileIterator.FileIterator

autoClose, countNewLineChars, debug, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose

Constructor Summary

Constructors

Constructor	Description
MarkerFileIterator(java.io.BufferedReader reader, int inOffset)
MarkerFileIterator(java.lang.String fileName, int inOffset)
MarkerFileIterator(java.lang.String fileName, Genome genome, int inOffset)

Method Summary

Modifier and Type	Method	Description
Chromosome	getChromosome(java.lang.String chromoName)	Find chromosome 'chromoName'.
Genome	getGenome()
protected void	init(java.lang.String fileName, int inOffset)	Initialize
boolean	isIgnoreChromosomeErrors()
Markers	loadMarkers()
int	parsePosition(java.lang.String posStr)	Parse a string as a 'position'.
void	sanityCheckChromo(java.lang.String chromoName, Chromosome chromo)	Sanity check
void	setCreateChromos(boolean createChromos)
void	setIgnoreChromosomeErrors(boolean ignoreChromosomeErrors)
void	setInOffset(int inOffset)

Methods inherited from class org.snpeff.fileIterator.FileIterator

close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, isDebug, iterator, load, next, readLine, readNext, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

createChromos

protected boolean createChromos

genome

protected Genome genome

ignoreChromosomeErrors

protected boolean ignoreChromosomeErrors

inOffset

protected int inOffset

Constructor Detail

MarkerFileIterator

public MarkerFileIterator(java.io.BufferedReader reader,
                          int inOffset)

MarkerFileIterator

public MarkerFileIterator(java.lang.String fileName,
                          Genome genome,
                          int inOffset)

MarkerFileIterator

public MarkerFileIterator(java.lang.String fileName,
                          int inOffset)

Method Detail

getChromosome

public Chromosome getChromosome(java.lang.String chromoName)

Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created

getGenome

public Genome getGenome()

init

protected void init(java.lang.String fileName,
                    int inOffset)

Initialize

Overrides:

init in class FileIterator<M extends Marker>

Parameters:

fileName - : Can be null (no file is opened)

isIgnoreChromosomeErrors

public boolean isIgnoreChromosomeErrors()

loadMarkers

public Markers loadMarkers()

parsePosition

public int parsePosition(java.lang.String posStr)

Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based

sanityCheckChromo

public void sanityCheckChromo(java.lang.String chromoName,
                              Chromosome chromo)

Sanity check

setCreateChromos

public void setCreateChromos(boolean createChromos)

setIgnoreChromosomeErrors

public void setIgnoreChromosomeErrors(boolean ignoreChromosomeErrors)

setInOffset

public void setInOffset(int inOffset)