org.broadinstitute.hellbender.utils.codecs

Class LineIteratorReader

java.lang.Object

java.io.Reader

org.broadinstitute.hellbender.utils.codecs.LineIteratorReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, java.lang.Readable

public class LineIteratorReader
extends java.io.Reader

A reader wrapper around a LineIterator.

This class is useful to implement codecs for formats for which a Reader based parser already exists.

Field Summary

Fields inherited from class java.io.Reader

lock

Constructor Summary

Constructors

Constructor and Description
LineIteratorReader(htsjdk.tribble.readers.LineIterator lineIterator)

Method Summary

Modifier and Type	Method and Description
void	close()
int	read(char[] cbuf, int off, int len) Reads lines from the buffer, and if empty from the underlying line-iterator.

Methods inherited from class java.io.Reader

mark, markSupported, read, read, read, ready, reset, skip

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LineIteratorReader

public LineIteratorReader(htsjdk.tribble.readers.LineIterator lineIterator)

Method Detail

read

public int read(char[] cbuf,
                int off,
                int len)

Reads lines from the buffer, and if empty from the underlying line-iterator.

Specified by:

read in class java.io.Reader

Parameters:

cbuf - the destination buffer.

off - the start position in the buffer to copy characters into.

len - number of characters to read.

Returns:

never less than 0 as this buffer never ends.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class java.io.Reader

Throws:

java.io.IOException