loci.common

Class StreamHandle

java.lang.Object

loci.common.StreamHandle

All Implemented Interfaces:

DataInput, DataOutput, IRandomAccess

Direct Known Subclasses:

BZip2Handle, GZipHandle, S3Handle, URLHandle, ZipHandle

public abstract class StreamHandle
extends Object
implements IRandomAccess

Abstract IRandomAccess implementation for reading from InputStreams and writing to OutputStreams.

Author:

Melissa Linkert melissa at glencoesoftware.com

See Also:

IRandomAccess

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StreamHandle.Settings

Field Summary

Fields

Modifier and Type	Field and Description
protected String	file Name of the open stream.
protected long	fp Current position within the stream.
protected long	length Length of the stream.
protected long	mark Marked position within the stream.
protected ByteOrder	order Byte ordering of this stream.
protected DataOutputStream	outStream OutputStream to be used for writing.
protected DataInputStream	stream InputStream to be used for reading.

Constructor Summary

Constructors

Constructor and Description
StreamHandle() Construct a new StreamHandle.

Method Summary

Modifier and Type	Method and Description
void	close() Closes this random access stream and releases any system resources associated with the stream.
boolean	exists() Returns whether this refers to a valid object
long	getFilePointer() Returns the current offset in this stream.
ByteOrder	getOrder() Returns the current order (endianness) of the stream.
long	length() Returns the length of this stream.
int	read(byte[] b) Reads up to b.length bytes of data from this stream into an array of bytes.
int	read(byte[] b, int off, int len) Reads up to len bytes of data from this stream into an array of bytes.
int	read(ByteBuffer buffer) Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
int	read(ByteBuffer buffer, int off, int len) Reads up to len bytes of data from this stream into a ByteBuffer.
boolean	readBoolean()
byte	readByte()
char	readChar()
double	readDouble()
float	readFloat()
void	readFully(byte[] b)
void	readFully(byte[] b, int off, int len)
int	readInt()
String	readLine()
long	readLong()
short	readShort()
int	readUnsignedByte()
int	readUnsignedShort()
String	readUTF()
protected abstract void	resetStream() Close and reopen the stream; the stream pointer and mark should be reset to 0.
void	seek(long pos) Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.
void	setOrder(ByteOrder order) Sets the byte order (endianness) of the stream.
int	skipBytes(int n)
long	skipBytes(long n) A long variant of DataInput.skipBytes(int).
void	write(byte[] b)
void	write(byte[] b, int off, int len)
void	write(ByteBuffer buf) Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
void	write(ByteBuffer buf, int off, int len) Writes up to len bytes of data from the given ByteBuffer to this stream.
void	write(int b)
void	writeBoolean(boolean v)
void	writeByte(int v)
void	writeBytes(String s)
void	writeChar(int v)
void	writeChars(String s)
void	writeDouble(double v)
void	writeFloat(float v)
void	writeInt(int v)
void	writeLong(long v)
void	writeShort(int v)
void	writeUTF(String str)

Methods inherited from class java.lang.Object

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

Field Detail

file

protected String file

Name of the open stream.

stream

protected DataInputStream stream

InputStream to be used for reading.

outStream

protected DataOutputStream outStream

OutputStream to be used for writing.

length

protected long length

Length of the stream.

fp

protected long fp

Current position within the stream.

mark

protected long mark

Marked position within the stream.

order

protected ByteOrder order

Byte ordering of this stream.

Constructor Detail

StreamHandle

public StreamHandle()

Construct a new StreamHandle. The file pointer will be set to 0, and the byte ordering will be big-endian.

Method Detail

close

public void close()
           throws IOException

Description copied from interface: IRandomAccess

Closes this random access stream and releases any system resources associated with the stream.

Specified by:

close in interface IRandomAccess

Throws:

IOException - if the underlying stream(s) could not be closed

getFilePointer

public long getFilePointer()
                    throws IOException

Description copied from interface: IRandomAccess

Returns the current offset in this stream.

Specified by:

getFilePointer in interface IRandomAccess

Returns:

the current byte offset within the file; expected to be non-negative and less than the value of #length()

Throws:

IOException - if the offset cannot be retrieved

exists

public boolean exists()
               throws IOException

Description copied from interface: IRandomAccess

Returns whether this refers to a valid object

Specified by:

exists in interface IRandomAccess

Returns:

true if this refers to a valid object

Throws:

IOException - if unable to determine whether the object is valid

length

public long length()
            throws IOException

Description copied from interface: IRandomAccess

Returns the length of this stream.

Specified by:

length in interface IRandomAccess

Returns:

the length in bytes of the stream

Throws:

IOException - if the length cannot be retrieved

read

public int read(byte[] b)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to b.length bytes of data from this stream into an array of bytes.

Specified by:

read in interface IRandomAccess

Parameters:

b - the array to fill from this stream

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

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

Description copied from interface: IRandomAccess

Reads up to len bytes of data from this stream into an array of bytes.

Specified by:

read in interface IRandomAccess

Parameters:

b - the array to fill from this stream

off - the offset in b from which to start filling; expected to be non-negative and no greater than b.length - len

len - the number of bytes to read; expected to be positive and no greater than b.length - offset

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

public int read(ByteBuffer buffer)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.

Specified by:

read in interface IRandomAccess

Parameters:

buffer - the ByteBuffer to fill from this stream

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

public int read(ByteBuffer buffer,
                int off,
                int len)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to len bytes of data from this stream into a ByteBuffer.

Specified by:

read in interface IRandomAccess

Parameters:

buffer - the ByteBuffer to fill from this stream

off - the offset in b from which to start filling; expected to be non-negative and no greater than buffer.capacity() - len

len - the number of bytes to read; expected to be positive and no greater than buffer.capacity() - offset

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

seek

public void seek(long pos)
          throws IOException

Description copied from interface: IRandomAccess

Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.

Specified by:

seek in interface IRandomAccess

Parameters:

pos - new byte offset (pointer) in the current stream. Unless otherwise noted, may be larger or smaller than the current pointer, but must be non-negative and less than the value of #length()

Throws:

IOException - if pos is invalid or the seek fails

See Also:

IRandomAccess.getFilePointer()

write

public void write(ByteBuffer buf)
           throws IOException

Description copied from interface: IRandomAccess

Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.

Specified by:

write in interface IRandomAccess

Parameters:

buf - the ByteBuffer containing bytes to write to this stream

Throws:

IOException - if writing is not possible

write

public void write(ByteBuffer buf,
                  int off,
                  int len)
           throws IOException

Description copied from interface: IRandomAccess

Writes up to len bytes of data from the given ByteBuffer to this stream.

Specified by:

write in interface IRandomAccess

Parameters:

buf - the ByteBuffer containing bytes to write to this stream

off - the offset in b from which to start writing; expected to be non-negative and no greater than buf.capacity() - len

len - the number of bytes to write; expected to be positive and no greater than buf.capacity() - offset

Throws:

IOException - if writing is not possible

getOrder

public ByteOrder getOrder()

Description copied from interface: IRandomAccess

Returns the current order (endianness) of the stream.

Specified by:

getOrder in interface IRandomAccess

Returns:

See above.

setOrder

public void setOrder(ByteOrder order)

Description copied from interface: IRandomAccess

Sets the byte order (endianness) of the stream.

Specified by:

setOrder in interface IRandomAccess

Parameters:

order - Order to set.

readBoolean

public boolean readBoolean()
                    throws IOException

Specified by:

readBoolean in interface DataInput

Throws:

IOException

readByte

public byte readByte()
              throws IOException

Specified by:

readByte in interface DataInput

Throws:

IOException

readChar

public char readChar()
              throws IOException

Specified by:

readChar in interface DataInput

Throws:

IOException

readDouble

public double readDouble()
                  throws IOException

Specified by:

readDouble in interface DataInput

Throws:

IOException

readFloat

public float readFloat()
                throws IOException

Specified by:

readFloat in interface DataInput

Throws:

IOException

readFully

public void readFully(byte[] b)
               throws IOException

Specified by:

readFully in interface DataInput

Throws:

IOException

readFully

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

Specified by:

readFully in interface DataInput

Throws:

IOException

readInt

public int readInt()
            throws IOException

Specified by:

readInt in interface DataInput

Throws:

IOException

readLine

public String readLine()
                throws IOException

Specified by:

readLine in interface DataInput

Throws:

IOException

readLong

public long readLong()
              throws IOException

Specified by:

readLong in interface DataInput

Throws:

IOException

readShort

public short readShort()
                throws IOException

Specified by:

readShort in interface DataInput

Throws:

IOException

readUnsignedByte

public int readUnsignedByte()
                     throws IOException

Specified by:

readUnsignedByte in interface DataInput

Throws:

IOException

readUnsignedShort

public int readUnsignedShort()
                      throws IOException

Specified by:

readUnsignedShort in interface DataInput

Throws:

IOException

readUTF

public String readUTF()
               throws IOException

Specified by:

readUTF in interface DataInput

Throws:

IOException

skipBytes

public int skipBytes(int n)
              throws IOException

Specified by:

skipBytes in interface DataInput

Throws:

IOException

skipBytes

public long skipBytes(long n)
               throws IOException

Description copied from interface: IRandomAccess

A long variant of DataInput.skipBytes(int).

Specified by:

skipBytes in interface IRandomAccess

Parameters:

n - the number of bytes to skip

Returns:

the number of bytes skipped

Throws:

IOException - if the operation failed

write

public void write(byte[] b)
           throws IOException

Specified by:

write in interface DataOutput

Throws:

IOException

write

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

Specified by:

write in interface DataOutput

Throws:

IOException

write

public void write(int b)
           throws IOException

Specified by:

write in interface DataOutput

Throws:

IOException

writeBoolean

public void writeBoolean(boolean v)
                  throws IOException

Specified by:

writeBoolean in interface DataOutput

Throws:

IOException

writeByte

public void writeByte(int v)
               throws IOException

Specified by:

writeByte in interface DataOutput

Throws:

IOException

writeBytes

public void writeBytes(String s)
                throws IOException

Specified by:

writeBytes in interface DataOutput

Throws:

IOException

writeChar

public void writeChar(int v)
               throws IOException

Specified by:

writeChar in interface DataOutput

Throws:

IOException

writeChars

public void writeChars(String s)
                throws IOException

Specified by:

writeChars in interface DataOutput

Throws:

IOException

writeDouble

public void writeDouble(double v)
                 throws IOException

Specified by:

writeDouble in interface DataOutput

Throws:

IOException

writeFloat

public void writeFloat(float v)
                throws IOException

Specified by:

writeFloat in interface DataOutput

Throws:

IOException

writeInt

public void writeInt(int v)
              throws IOException

Specified by:

writeInt in interface DataOutput

Throws:

IOException

writeLong

public void writeLong(long v)
               throws IOException

Specified by:

writeLong in interface DataOutput

Throws:

IOException

writeShort

public void writeShort(int v)
                throws IOException

Specified by:

writeShort in interface DataOutput

Throws:

IOException

writeUTF

public void writeUTF(String str)
              throws IOException

Specified by:

writeUTF in interface DataOutput

Throws:

IOException

resetStream

protected abstract void resetStream()
                             throws IOException

Close and reopen the stream; the stream pointer and mark should be reset to 0. This method is called if we need to seek backwards within the stream.

Throws:

IOException - if the stream cannot be reset