ch.systemsx.cisd.hdf5.io

Class HDF5DataSetRandomAccessFile

java.lang.Object

ch.systemsx.cisd.hdf5.io.HDF5DataSetRandomAccessFile

All Implemented Interfaces:

ch.systemsx.cisd.base.io.ICloseable, 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

Methods

Modifier and Type	Method and Description
int	available()
void	close()
void	flush()
java.nio.ByteOrder	getByteOrder()
java.lang.String	getDataSetPath()
long	getFilePointer()
java.io.File	getHdf5File()
boolean	isReadOnly() Returns true if the HDF5 file has been opened in read-only mode.
long	length()
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)
void	setByteOrder(java.nio.ByteOrder byteOrder)
void	setLength(long newLength)
long	skip(long n)
int	skipBytes(int n)
void	synchronize()
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

Specified by:

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

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

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

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

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

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

available

public int available()

Specified by:

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

close

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

Specified by:

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

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

mark

public void mark(int readlimit)

Specified by:

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

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

markSupported

public boolean markSupported()

Specified by:

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

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

synchronize

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

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

getByteOrder

public java.nio.ByteOrder getByteOrder()

Specified by:

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

setByteOrder

public void setByteOrder(java.nio.ByteOrder byteOrder)

Specified by:

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

seek

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

Specified by:

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

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

length

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

Specified by:

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

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

setLength

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

Specified by:

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

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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