com.intel.genomicsdb

Class SilentByteBufferStream

java.lang.Object

java.io.OutputStream

com.intel.genomicsdb.SilentByteBufferStream

All Implemented Interfaces:

Closeable, Flushable, AutoCloseable

class SilentByteBufferStream
extends OutputStream

Buffer stream implementation - it's silent in the sense that when the buffer is full, it doesn't raise an exception but just marks a a flag as full. It's up to the caller to check the flag and retry later Why? Most likely, it's faster to check a flag rather than throw and catch an exception

Field Summary

Fields

Modifier and Type	Field and Description
private byte[]	mBuffer
private long	mMarker
private long	mNumValidBytes
private boolean	mOverflow

Constructor Summary

Constructors

Constructor and Description
SilentByteBufferStream() Constructor - uses default value of buffer capacity (20KiB)
SilentByteBufferStream(long capacity) Constructor - uses specified buffer capacity

Method Summary

Modifier and Type	Method and Description
void	close()
void	flush()
byte[]	getBuffer() Get byte buffer for this stream
long	getMarker() Get marker value
long	getNumValidBytes() Get number of valid bytes
boolean	overflow() Returns if the buffer has overflowed
void	resize(long newSize) Resizes buffer to new size - data is retained
void	setMarker(long value) Caller code can use this function to mark a certain point in the buffer This is generally used to mark the position in the buffer after the last complete VariantContext object written
void	setNumValidBytes(long value) Set number of valid bytes
void	setOverflow(boolean value) Set overflow value
int	size() Returns buffer capacity in bytes
void	write(byte[] b)
void	write(byte[] b, int off, int len)
void	write(int b)

Methods inherited from class java.lang.Object

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

Field Detail

mBuffer

private byte[] mBuffer

mNumValidBytes

private long mNumValidBytes

mMarker

private long mMarker

mOverflow

private boolean mOverflow

Constructor Detail

SilentByteBufferStream

public SilentByteBufferStream()

Constructor - uses default value of buffer capacity (20KiB)

SilentByteBufferStream

public SilentByteBufferStream(long capacity)

Constructor - uses specified buffer capacity

Parameters:

capacity - size of buffer in bytes

Method Detail

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class OutputStream

Throws:

IOException

flush

public void flush()
           throws IOException

Specified by:

flush in interface Flushable

Overrides:

flush in class OutputStream

Throws:

IOException

write

public void write(byte[] b,
                  int off,
                  int len)
           throws IOException

Overrides:

write in class OutputStream

Throws:

IOException

write

public void write(byte[] b)
           throws IOException

Overrides:

write in class OutputStream

Throws:

IOException

write

public void write(int b)
           throws IOException

Specified by:

write in class OutputStream

Throws:

IOException

size

public int size()

Returns buffer capacity in bytes

Returns:

buffer capacity in bytes

resize

public void resize(long newSize)

Resizes buffer to new size - data is retained

Parameters:

newSize - new capacity of the buffer

overflow

public boolean overflow()

Returns if the buffer has overflowed

Returns:

true if the buffer has overflowed

setOverflow

public void setOverflow(boolean value)

Set overflow value

Parameters:

value - overflow value

getNumValidBytes

public long getNumValidBytes()

Get number of valid bytes

Returns:

number of valid bytes

setNumValidBytes

public void setNumValidBytes(long value)

Set number of valid bytes

Parameters:

value - number of valid bytes

setMarker

public void setMarker(long value)

Caller code can use this function to mark a certain point in the buffer This is generally used to mark the position in the buffer after the last complete VariantContext object written

Parameters:

value - set marker value

getMarker

public long getMarker()

Get marker value

Returns:

marker value

getBuffer

public byte[] getBuffer()

Get byte buffer for this stream

Returns:

byte buffer for this stream