ch.systemsx.cisd.hdf5.io

Class HDF5DataSetRandomAccessFile

java.lang.Object

ch.systemsx.cisd.hdf5.io.HDF5DataSetRandomAccessFile

All Implemented Interfaces:

ch.systemsx.cisd.base.io.IInputStream, ch.systemsx.cisd.base.io.IOutputStream, ch.systemsx.cisd.base.io.IRandomAccessFile, ch.systemsx.cisd.base.io.ISynchronizable, java.io.Closeable, java.io.DataInput, java.io.DataOutput, java.io.Flushable, java.lang.AutoCloseable

public class HDF5DataSetRandomAccessFile
extends java.lang.Object
implements ch.systemsx.cisd.base.io.IRandomAccessFile, java.io.Flushable

A IRandomAccessFile backed by an HDF5 dataset. The HDF5 dataset needs to be a byte array (or opaque byte array) of rank 1.

Method Summary

Modifier and Type	Method and Description
int	available()
void	close()
void	flush()
java.nio.ByteOrder	getByteOrder() Gets the byte-order (endiness) of the random access file.
java.lang.String	getDataSetPath()
long	getFilePointer() Returns the current offset in this file.
java.io.File	getHdf5File()
boolean	isReadOnly() Returns true if the HDF5 file has been opened in read-only mode.
long	length() Returns the length of this file.
void	mark(int readlimit)
boolean	markSupported()
int	read()
int	read(byte[] b)
int	read(byte[] b, int off, int len)
boolean	readBoolean()
byte	readByte()
char	readChar()
double	readDouble()
float	readFloat()
void	readFully(byte[] b)
void	readFully(byte[] b, int off, int len)
int	readInt()
java.lang.String	readLine()
long	readLong()
short	readShort()
int	readUnsignedByte()
int	readUnsignedShort()
java.lang.String	readUTF()
void	reset()
void	seek(long pos) Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
void	setByteOrder(java.nio.ByteOrder byteOrder) Sets the byte-order (endiness) of the random access file.
void	setLength(long newLength) Sets the length of this file.
long	skip(long n)
int	skipBytes(int n)
void	synchronize() Performs a synchronization of the resource.
void	write(byte[] b)
void	write(byte[] b, int off, int len)
void	write(int b)
void	writeBoolean(boolean v)
void	writeByte(int v)
void	writeBytes(java.lang.String s)
void	writeChar(int v)
void	writeChars(java.lang.String s)
void	writeDouble(double v)
void	writeFloat(float v)
void	writeInt(int v)
void	writeLong(long v)
void	writeShort(int v)
void	writeUTF(java.lang.String str)

Methods inherited from class java.lang.Object

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

Method Detail

getHdf5File

public java.io.File getHdf5File()

getDataSetPath

public java.lang.String getDataSetPath()

isReadOnly

public boolean isReadOnly()

Returns true if the HDF5 file has been opened in read-only mode.

getFilePointer

public long getFilePointer()
                    throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Returns the current offset in this file.

Specified by:

getFilePointer in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Returns:

the offset from the beginning of the file, in bytes, at which the next read or write occurs.

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked - if an I/O error occurs.

read

public int read()
         throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

read in interface ch.systemsx.cisd.base.io.IInputStream

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.read()

read

public int read(byte[] b)
         throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

read in interface ch.systemsx.cisd.base.io.IInputStream

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.read(byte[])

read

public int read(byte[] b,
                int off,
                int len)
         throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

read in interface ch.systemsx.cisd.base.io.IInputStream

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.read(byte[], int, int)

skip

public long skip(long n)
          throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

skip in interface ch.systemsx.cisd.base.io.IInputStream

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.skip(long)

available

public int available()

Specified by:

available in interface ch.systemsx.cisd.base.io.IInputStream

See Also:

InputStream.available()

close

public void close()
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

close in interface ch.systemsx.cisd.base.io.IInputStream

Specified by:

close in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.close()

mark

public void mark(int readlimit)

Specified by:

mark in interface ch.systemsx.cisd.base.io.IInputStream

See Also:

InputStream.mark(int)

reset

public void reset()
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

reset in interface ch.systemsx.cisd.base.io.IInputStream

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

InputStream.reset()

markSupported

public boolean markSupported()

Specified by:

markSupported in interface ch.systemsx.cisd.base.io.IInputStream

See Also:

InputStream.markSupported()

flush

public void flush()
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

flush in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

flush in interface java.io.Flushable

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

OutputStream.flush()

synchronize

public void synchronize()
                 throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: ch.systemsx.cisd.base.io.ISynchronizable

Performs a synchronization of the resource.

Specified by:

synchronize in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

synchronize in interface ch.systemsx.cisd.base.io.ISynchronizable

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

OutputStream.flush()

getByteOrder

public java.nio.ByteOrder getByteOrder()

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Gets the byte-order (endiness) of the random access file. Default is network-byte order (big-endian).

Specified by:

getByteOrder in interface ch.systemsx.cisd.base.io.IRandomAccessFile

setByteOrder

public void setByteOrder(java.nio.ByteOrder byteOrder)

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Sets the byte-order (endiness) of the random access file.

Specified by:

setByteOrder in interface ch.systemsx.cisd.base.io.IRandomAccessFile

seek

public void seek(long pos)
          throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs. The offset may be set beyond the end of the file. Setting the offset beyond the end of the file does not change the file length. The file length will change only by writing after the offset has been set beyond the end of the file.

Specified by:

seek in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Parameters:

pos - the offset position, measured in bytes from the beginning of the file, at which to set the file pointer.

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked - if pos is less than 0 or if an I/O error occurs.

length

public long length()
            throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Returns the length of this file.

Specified by:

length in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Returns:

the length of this file, measured in bytes.

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked - if an I/O error occurs.

setLength

public void setLength(long newLength)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: ch.systemsx.cisd.base.io.IRandomAccessFile

Sets the length of this file.

If the present length of the file as returned by the length method is greater than the newLength argument then the file will be truncated. In this case, if the file offset as returned by the getFilePointer method is greater than newLength then after this method returns the offset will be equal to newLength.

If the present length of the file as returned by the length method is smaller than the newLength argument then the file will be extended. In this case, the contents of the extended portion of the file are not defined.

Specified by:

setLength in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Parameters:

newLength - The desired length of the file

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked - If an I/O error occurs

readFully

public void readFully(byte[] b)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readFully in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readFully in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readFully(byte[])

readFully

public void readFully(byte[] b,
                      int off,
                      int len)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readFully in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readFully in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readFully(byte[], int, int)

skipBytes

public int skipBytes(int n)
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

skipBytes in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

skipBytes in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.skipBytes(int)

readBoolean

public boolean readBoolean()
                    throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readBoolean in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readBoolean in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readBoolean()

readByte

public byte readByte()
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readByte in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readByte in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readByte()

readUnsignedByte

public int readUnsignedByte()
                     throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readUnsignedByte in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readUnsignedByte in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readUnsignedByte()

readShort

public short readShort()
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readShort in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readShort in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readShort()

readUnsignedShort

public int readUnsignedShort()
                      throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readUnsignedShort in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readUnsignedShort in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readUnsignedShort()

readChar

public char readChar()
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readChar in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readChar in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readChar()

readInt

public int readInt()
            throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readInt in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readInt in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readInt()

readLong

public long readLong()
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readLong in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readLong in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readLong()

readFloat

public float readFloat()
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readFloat in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readFloat in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readFloat()

readDouble

public double readDouble()
                  throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readDouble in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readDouble in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readDouble()

readLine

public java.lang.String readLine()
                          throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readLine in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readLine in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readLine()

readUTF

public java.lang.String readUTF()
                         throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

readUTF in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

readUTF in interface java.io.DataInput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataInput.readUTF()

write

public void write(int b)
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

write in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

write in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

write in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.write(int)

write

public void write(byte[] b)
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

write in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

write in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

write in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.write(byte[])

write

public void write(byte[] b,
                  int off,
                  int len)
           throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

write in interface ch.systemsx.cisd.base.io.IOutputStream

Specified by:

write in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

write in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.write(byte[], int, int)

writeBoolean

public void writeBoolean(boolean v)
                  throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeBoolean in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeBoolean in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeBoolean(boolean)

writeByte

public void writeByte(int v)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeByte in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeByte in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeByte(int)

writeShort

public void writeShort(int v)
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeShort in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeShort in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeShort(int)

writeChar

public void writeChar(int v)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeChar in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeChar in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeChar(int)

writeInt

public void writeInt(int v)
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeInt in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeInt in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeInt(int)

writeLong

public void writeLong(long v)
               throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeLong in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeLong in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeLong(long)

writeFloat

public void writeFloat(float v)
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeFloat in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeFloat in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeFloat(float)

writeDouble

public void writeDouble(double v)
                 throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeDouble in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeDouble in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeDouble(double)

writeBytes

public void writeBytes(java.lang.String s)
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeBytes in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeBytes in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeBytes(String)

writeChars

public void writeChars(java.lang.String s)
                throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeChars in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeChars in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeChars(String)

writeUTF

public void writeUTF(java.lang.String str)
              throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Specified by:

writeUTF in interface ch.systemsx.cisd.base.io.IRandomAccessFile

Specified by:

writeUTF in interface java.io.DataOutput

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

See Also:

DataOutput.writeUTF(String)