Package org.snpeff.fileIterator
Class MarkerFileIterator<M extends Marker>
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<M>
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- org.snpeff.fileIterator.MarkerFileIterator<M>
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- 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
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Field Summary
Fields Modifier and Type Field Description protected boolean
createChromos
protected Genome
genome
protected boolean
ignoreChromosomeErrors
protected int
inOffset
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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)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
Initializeboolean
isIgnoreChromosomeErrors()
Markers
loadMarkers()
int
parsePosition(java.lang.String posStr)
Parse a string as a 'position'.void
sanityCheckChromo(java.lang.String chromoName, Chromosome chromo)
Sanity checkvoid
setCreateChromos(boolean createChromos)
void
setIgnoreChromosomeErrors(boolean ignoreChromosomeErrors)
void
setInOffset(int inOffset)
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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
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Field Detail
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createChromos
protected boolean createChromos
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genome
protected Genome genome
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ignoreChromosomeErrors
protected boolean ignoreChromosomeErrors
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inOffset
protected int inOffset
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Constructor Detail
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MarkerFileIterator
public MarkerFileIterator(java.io.BufferedReader reader, int inOffset)
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MarkerFileIterator
public MarkerFileIterator(java.lang.String fileName, Genome genome, int inOffset)
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MarkerFileIterator
public MarkerFileIterator(java.lang.String fileName, int inOffset)
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Method Detail
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getChromosome
public Chromosome getChromosome(java.lang.String chromoName)
Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created
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getGenome
public Genome getGenome()
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init
protected void init(java.lang.String fileName, int inOffset)
Initialize- Overrides:
init
in classFileIterator<M extends Marker>
- Parameters:
fileName
- : Can be null (no file is opened)
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isIgnoreChromosomeErrors
public boolean isIgnoreChromosomeErrors()
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loadMarkers
public Markers loadMarkers()
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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
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sanityCheckChromo
public void sanityCheckChromo(java.lang.String chromoName, Chromosome chromo)
Sanity check
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setCreateChromos
public void setCreateChromos(boolean createChromos)
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setIgnoreChromosomeErrors
public void setIgnoreChromosomeErrors(boolean ignoreChromosomeErrors)
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setInOffset
public void setInOffset(int inOffset)
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