Package org.snpeff.fileIterator

Class FileIterator<T>

java.lang.Object

org.snpeff.fileIterator.FileIterator<T>

All Implemented Interfaces:

java.lang.Iterable<T>, java.util.Iterator<T>

Direct Known Subclasses:

FastaFileIterator, LineClassFileIterator, LineFileIterator, MarkerFileIterator, PedFileIterator, SamFileIterator

public abstract class FileIterator<T>
extends java.lang.Object
implements java.lang.Iterable<T>, java.util.Iterator<T>

Opens a file and iterates over all objects in the file Note: The file is not loaded in memory, thus allows to iterate over very large files

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	autoClose
protected int	countNewLineChars
protected boolean	debug
protected java.lang.String	fileName
protected long	fileSize
protected java.lang.String	line
protected int	lineNum
protected T	next
protected java.lang.String	nextLine
protected java.io.BufferedReader	reader
protected boolean	verbose

Constructor Summary

Constructors

Constructor	Description
FileIterator(java.io.BufferedReader reader)
FileIterator(java.lang.String fileName)

Method Summary

Modifier and Type	Method	Description
void	close()	Close file
protected int	countNewLineChars()	Guess number of newline characters used (e.g.
long	getFilePointer()	Get position within file
java.lang.String	getLine()
int	getLineNum()
protected void	guessNewLineChars()	Guess number of newline characters used (e.g.
boolean	hasNext()
boolean	hasSeek()	Is 'seek' operation supported?
protected void	init(java.lang.String fileName, int inOffset)	Initialize
boolean	isDebug()
java.util.Iterator<T>	iterator()
java.util.List<T>	load()	Load all elements from a file into a list
T	next()
protected java.lang.String	readLine()	Read a line from reader
protected abstract T	readNext()	Read next element
protected boolean	ready()	Is reader ready? I.e.
void	remove()
void	seek(long pos)	Seek to 'pos' (jump to byte number 'pos' in the file
void	setAutoClose(boolean autoClose)
void	setDebug(boolean debug)
void	setVerbose(boolean verbose)
java.lang.String	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 Detail

debug

protected boolean debug

verbose

protected boolean verbose

autoClose

protected boolean autoClose

countNewLineChars

protected int countNewLineChars

lineNum

protected int lineNum

next

protected T next

reader

protected java.io.BufferedReader reader

fileName

protected java.lang.String fileName

line

protected java.lang.String line

nextLine

protected java.lang.String nextLine

fileSize

protected long fileSize

Constructor Detail

FileIterator

public FileIterator(java.io.BufferedReader reader)

FileIterator

public FileIterator(java.lang.String fileName)

Method Detail

close

public void close()

Close file

countNewLineChars

protected int countNewLineChars()

Guess number of newline characters used (e.g. '\n' or '\r\n'

getFilePointer

public long getFilePointer()

Get position within file

getLine

public java.lang.String getLine()

getLineNum

public int getLineNum()

guessNewLineChars

protected void guessNewLineChars()

Guess number of newline characters used (e.g. '\n' or '\r\n' Make sure we return to the current read position

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<T>

hasSeek

public boolean hasSeek()

Is 'seek' operation supported?

init

protected void init(java.lang.String fileName,
                    int inOffset)

Initialize

Parameters:

fileName - : Can be null (no file is opened)

isDebug

public boolean isDebug()

iterator

public java.util.Iterator<T> iterator()

Specified by:

iterator in interface java.lang.Iterable<T>

load

public java.util.List<T> load()

Load all elements from a file into a list

next

public T next()

Specified by:

next in interface java.util.Iterator<T>

readLine

protected java.lang.String readLine()
                             throws java.io.IOException

Read a line from reader

Throws:

java.io.IOException

readNext

protected abstract T readNext()

Read next element

ready

protected boolean ready()
                 throws java.io.IOException

Is reader ready? I.e. Can we read a line?

Throws:

java.io.IOException

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<T>

seek

public void seek(long pos)
          throws java.io.IOException

Seek to 'pos' (jump to byte number 'pos' in the file

Throws:

java.io.IOException

setAutoClose

public void setAutoClose(boolean autoClose)

setDebug

public void setDebug(boolean debug)

setVerbose

public void setVerbose(boolean verbose)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object