RegulationFileIterator (SnpEff 5.2 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<M>

org.snpeff.fileIterator.MarkerFileIterator<Regulation>

org.snpeff.fileIterator.RegulationFileIterator

All Implemented Interfaces:: Iterable<Regulation>, Iterator<Regulation>

Direct Known Subclasses:: RegulationBedFileIterator, RegulationGffFileIterator

public abstract class RegulationFileIterator extends MarkerFileIterator<Regulation>

Opens a regulation file and create Regulation elements.

Author:: pcingola

Field Summary

Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, 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

RegulationFileIterator(String fileName, int inOffset)

RegulationFileIterator(String fileName, Genome genome, int inOffset)
Method Summary

Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator
getChromosome, getGenome, init, isIgnoreChromosomeErrors, loadMarkers, parsePosition, sanityCheckChromo, setCreateChromos, setIgnoreChromosomeErrors, setInOffset

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

Constructor Details
- RegulationFileIterator
  
  public RegulationFileIterator(String fileName, Genome genome, int inOffset)
- RegulationFileIterator
  
  public RegulationFileIterator(String fileName, int inOffset)