Package org.snpeff.fileIterator
Class RegulationGffFileIterator
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<M>
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- org.snpeff.fileIterator.MarkerFileIterator<Regulation>
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- org.snpeff.fileIterator.RegulationFileIterator
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- org.snpeff.fileIterator.RegulationGffFileIterator
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- All Implemented Interfaces:
java.lang.Iterable<Regulation>
,java.util.Iterator<Regulation>
public class RegulationGffFileIterator extends RegulationFileIterator
Opens a GFF3 file and create regulatory elements. Example of regulatory GFF file: ftp://ftp.ensembl.org/pub/release-63/regulation/homo_sapiens/AnnotatedFeatures.gff.gz References (GFF3) : http://www.sequenceontology.org/gff3.shtml- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
GFF_OFFSET
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Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
Constructors Constructor Description RegulationGffFileIterator(java.lang.String fileName)
RegulationGffFileIterator(java.lang.String fileName, Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected Regulation
readNext()
Read next element-
Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator
getChromosome, getGenome, init, isIgnoreChromosomeErrors, loadMarkers, parsePosition, sanityCheckChromo, setCreateChromos, setIgnoreChromosomeErrors, setInOffset
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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, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
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Field Detail
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GFF_OFFSET
public static final int GFF_OFFSET
- See Also:
- Constant Field Values
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Constructor Detail
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RegulationGffFileIterator
public RegulationGffFileIterator(java.lang.String fileName)
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RegulationGffFileIterator
public RegulationGffFileIterator(java.lang.String fileName, Genome genome)
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Method Detail
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readNext
protected Regulation readNext()
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Regulation>
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