MotifFileIterator (SnpEff 5.1 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<M>

org.snpeff.fileIterator.MarkerFileIterator<Motif>

org.snpeff.fileIterator.MotifFileIterator

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

public class MotifFileIterator extends MarkerFileIterator<Motif>

Opens a regulation file and create Motif elements.

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static final int

GFF_OFFSET

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

MotifFileIterator(String fileName, Genome genome, Jaspar jaspar)
Method Summary

Modifier and Type

Method

Description

protected Motif

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

Field Details
- GFF_OFFSET
  
  public static final int GFF_OFFSET
  See Also:
  
  Constant Field Values
Constructor Details
- MotifFileIterator
  
  public MotifFileIterator(String fileName, Genome genome, Jaspar jaspar)
Method Details
- readNext
  
  protected Motif readNext()
  
  Description copied from class: FileIterator
  
  Read next element
  
  Specified by:
  
  readNext in class FileIterator<Motif>