LineFileIterator (SnpEff 5.2 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<String>

org.snpeff.fileIterator.LineFileIterator

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

Direct Known Subclasses:: LineSeqFileIterator

public class LineFileIterator extends FileIterator<String>

Iterate on each line in this file

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static boolean

debug

Fields inherited from class org.snpeff.fileIterator.FileIterator
autoClose, countNewLineChars, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose
Constructor Summary

Constructors

Constructor

Description

LineFileIterator(String lineSeqFileName)

LineFileIterator(String lineSeqFileName, boolean gzip)
Method Summary

Modifier and Type

Method

Description

Iterator<String>

iterator()

protected String

readNext()

Read a sequence from the file

Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, 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
- debug
  
  public static boolean debug
Constructor Details
- LineFileIterator
  
  public LineFileIterator(String lineSeqFileName)
- LineFileIterator
  
  public LineFileIterator(String lineSeqFileName, boolean gzip)
Method Details
- iterator
  
  public Iterator<String> iterator()
  
  Specified by:
  
  iterator in interface Iterable<String>
  
  Overrides:
  
  iterator in class FileIterator<String>
- readNext
  
  protected String readNext()
  
  Read a sequence from the file
  
  Specified by:
  
  readNext in class FileIterator<String>
  
  Returns: