picard.illumina.parser.readers

Class MMapBackedIteratorFactory

java.lang.Object

picard.illumina.parser.readers.MMapBackedIteratorFactory

public class MMapBackedIteratorFactory
extends java.lang.Object

MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header). Values provided by the MMappedBinaryFileReader are read as if they are little endian. Note (read to end): This class IS thread-safe and immutable though the iterator and ByteBuffers it produces are NOT. The values read are assumed to be signed, NO promoting/sign conversion happens in this class.

Constructor Summary

Constructors

Constructor and Description
MMapBackedIteratorFactory()

Method Summary

Modifier and Type	Method and Description
static picard.illumina.parser.readers.BinaryFileIterator<java.nio.ByteBuffer>	getByteBufferIterator(int headerSize, int elementSize, java.io.File binaryFile)
static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Byte>	getByteIterator(int headerSize, java.io.File binaryFile)
static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Float>	getFloatIterator(int headerSize, java.io.File binaryFile)
static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Integer>	getIntegerIterator(int headerSize, java.io.File binaryFile)
static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Long>	getLongIterator(int headerSize, java.io.File binaryFile)

Methods inherited from class java.lang.Object

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

Constructor Detail

MMapBackedIteratorFactory

public MMapBackedIteratorFactory()

Method Detail

getIntegerIterator

public static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Integer> getIntegerIterator(int headerSize,
                                                                                                      java.io.File binaryFile)

getByteIterator

public static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Byte> getByteIterator(int headerSize,
                                                                                                java.io.File binaryFile)

getFloatIterator

public static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Float> getFloatIterator(int headerSize,
                                                                                                  java.io.File binaryFile)

getLongIterator

public static picard.illumina.parser.readers.BinaryFileIterator<java.lang.Long> getLongIterator(int headerSize,
                                                                                                java.io.File binaryFile)

getByteBufferIterator

public static picard.illumina.parser.readers.BinaryFileIterator<java.nio.ByteBuffer> getByteBufferIterator(int headerSize,
                                                                                                           int elementSize,
                                                                                                           java.io.File binaryFile)