Gff3FileIterator (SnpEff 5.1 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<M>

org.snpeff.fileIterator.MarkerFileIterator<GffMarker>

org.snpeff.fileIterator.Gff3FileIterator

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

public class Gff3FileIterator extends MarkerFileIterator<GffMarker>

Opens a sequence change file and iterates over all intervals in GFF3 format.

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

Gff3FileIterator(String fileName)

Gff3FileIterator(String fileName, Genome genome)

Gff3FileIterator(String fileName, Genome genome, int inOffset)
Method Summary

Modifier and Type

Method

Description

protected GffMarker

readNext()

Read next element

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, 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
- Gff3FileIterator
  
  public Gff3FileIterator(String fileName)
- Gff3FileIterator
  
  public Gff3FileIterator(String fileName, Genome genome)
- Gff3FileIterator
  
  public Gff3FileIterator(String fileName, Genome genome, int inOffset)
Method Details
- readNext
  
  protected GffMarker readNext()
  
  Description copied from class: FileIterator
  
  Read next element
  
  Specified by:
  
  readNext in class FileIterator<GffMarker>