loci.common

Class RandomAccessInputStream

java.lang.Object

java.io.InputStream

loci.common.RandomAccessInputStream

All Implemented Interfaces:

com.esotericsoftware.kryo.KryoSerializable, java.io.Closeable, java.io.DataInput, java.lang.AutoCloseable

public class RandomAccessInputStream
extends java.io.InputStream
implements java.io.DataInput, java.io.Closeable, com.esotericsoftware.kryo.KryoSerializable

Top-level class for reading from various data sources.

Source code:

Trac, Gitweb

Author:

Melissa Linkert melissa at glencoesoftware.com, Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	DEFAULT_BLOCK_SIZE Block size to use when searching through the stream.
protected java.lang.String	encoding
protected java.lang.String	file The file name.
protected long	length
protected long	markedPos
protected static int	MAX_OVERHEAD Maximum size of the buffer used by the DataInputStream.
protected static int	MAX_SEARCH_SIZE Maximum number of bytes to search when searching through the stream.
protected IRandomAccess	raf

Constructor Summary

Constructors

Constructor and Description
RandomAccessInputStream(byte[] array) Constructs a random access stream around the given byte array.
RandomAccessInputStream(IRandomAccess handle) Constructs a random access stream around the given handle.
RandomAccessInputStream(IRandomAccess handle, java.lang.String file) Constructs a random access stream around the given handle, and with the associated file path.
RandomAccessInputStream(java.lang.String file) Constructs a hybrid RandomAccessFile/DataInputStream around the given file.
RandomAccessInputStream(java.lang.String file, int bufferSize) Constructs a hybrid RandomAccessFile/DataInputStream around the given file.

Method Summary

Methods

Modifier and Type	Method and Description
int	available()
void	close() Closes the streams.
java.lang.String	findString(boolean saveString, int blockSize, java.lang.String... terminators) Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
java.lang.String	findString(boolean saveString, java.lang.String... terminators) Reads or skips a string ending with one of the given terminating substrings.
java.lang.String	findString(int blockSize, java.lang.String... terminators) Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
java.lang.String	findString(java.lang.String... terminators) Reads a string ending with one of the given terminating substrings.
long	getFilePointer() Gets the current (absolute) file pointer.
boolean	isLittleEndian() Gets the endianness of the stream.
long	length() Gets the number of bytes in the file.
void	mark(int readLimit)
boolean	markSupported()
void	order(boolean little) Sets the endianness of the stream.
int	read()
int	read(byte[] array) Read bytes from the stream into the given array.
int	read(byte[] array, int offset, int n) Read n bytes from the stream into the given array at the specified offset.
int	read(java.nio.ByteBuffer buf) Read bytes from the stream into the given buffer.
int	read(java.nio.ByteBuffer buf, int offset, int n) Read n bytes from the stream into the given buffer at the specified offset.
void	read(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input in)
boolean	readBoolean() Read an input byte and return true if the byte is nonzero.
byte	readByte() Read one byte and return it.
char	readChar() Read an input char.
java.lang.String	readCString() Read a string of arbitrary length, terminated by a null char.
double	readDouble() Read eight bytes and return a double value.
float	readFloat() Read four bytes and return a float value.
void	readFully(byte[] array) Read bytes from the stream into the given array.
void	readFully(byte[] array, int offset, int n) Read n bytes from the stream into the given array at the specified offset.
int	readInt() Read four input bytes and return an int value.
java.lang.String	readLine() Read the next line of text from the input stream.
long	readLong() Read eight input bytes and return a long value.
short	readShort() Read two input bytes and return a short value.
java.lang.String	readString(int n) Read a string of up to length n.
java.lang.String	readString(java.lang.String lastChars) Reads a string ending with one of the characters in the given string.
int	readUnsignedByte() Read an input byte and zero extend it appropriately.
int	readUnsignedShort() Read two bytes and return an int in the range 0 through 65535.
java.lang.String	readUTF() Read a string that has been encoded using a modified UTF-8 format.
void	reset()
void	seek(long pos) Seeks to the given offset within the stream.
void	setEncoding(java.lang.String encoding) Sets the native encoding of the stream.
void	setLength(long newLength) Sets the length of the stream.
int	skipBytes(int n) Skip n bytes within the stream.
void	write(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output out)

Methods inherited from class java.io.InputStream

skip

Methods inherited from class java.lang.Object

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

Field Detail

MAX_OVERHEAD

protected static final int MAX_OVERHEAD

Maximum size of the buffer used by the DataInputStream.

See Also:

Constant Field Values

DEFAULT_BLOCK_SIZE

protected static final int DEFAULT_BLOCK_SIZE

Block size to use when searching through the stream.

See Also:

Constant Field Values

MAX_SEARCH_SIZE

protected static final int MAX_SEARCH_SIZE

Maximum number of bytes to search when searching through the stream.

See Also:

Constant Field Values

raf

protected IRandomAccess raf

file

protected java.lang.String file

The file name.

length

protected long length

markedPos

protected long markedPos

encoding

protected java.lang.String encoding

Constructor Detail

RandomAccessInputStream

public RandomAccessInputStream(java.lang.String file)
                        throws java.io.IOException

Constructs a hybrid RandomAccessFile/DataInputStream around the given file.

Throws:

java.io.IOException

RandomAccessInputStream

public RandomAccessInputStream(java.lang.String file,
                       int bufferSize)
                        throws java.io.IOException

Constructs a hybrid RandomAccessFile/DataInputStream around the given file.

Throws:

java.io.IOException

RandomAccessInputStream

public RandomAccessInputStream(IRandomAccess handle)
                        throws java.io.IOException

Constructs a random access stream around the given handle.

Throws:

java.io.IOException

RandomAccessInputStream

public RandomAccessInputStream(IRandomAccess handle,
                       java.lang.String file)
                        throws java.io.IOException

Constructs a random access stream around the given handle, and with the associated file path.

Throws:

java.io.IOException

RandomAccessInputStream

public RandomAccessInputStream(byte[] array)
                        throws java.io.IOException

Constructs a random access stream around the given byte array.

Throws:

java.io.IOException

Method Detail

setEncoding

public void setEncoding(java.lang.String encoding)

Sets the native encoding of the stream.

See Also:

Constants.ENCODING

seek

public void seek(long pos)
          throws java.io.IOException

Seeks to the given offset within the stream.

Throws:

java.io.IOException

length

public long length()
            throws java.io.IOException

Gets the number of bytes in the file.

Throws:

java.io.IOException

setLength

public void setLength(long newLength)
               throws java.io.IOException

Sets the length of the stream. The new length must be less than the real length of the stream. This allows us to work with a truncated view of a file, without modifying the file itself. Passing in a negative value will reset the length to the stream's real length.

Throws:

java.io.IOException

getFilePointer

public long getFilePointer()
                    throws java.io.IOException

Gets the current (absolute) file pointer.

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Closes the streams.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.InputStream

Throws:

java.io.IOException

order

public void order(boolean little)

Sets the endianness of the stream.

isLittleEndian

public boolean isLittleEndian()

Gets the endianness of the stream.

readString

public java.lang.String readString(java.lang.String lastChars)
                            throws java.io.IOException

Reads a string ending with one of the characters in the given string.

Throws:

java.io.IOException

See Also:

findString(String...)

findString

public java.lang.String findString(java.lang.String... terminators)
                            throws java.io.IOException

Reads a string ending with one of the given terminating substrings.

Parameters:

terminators - The strings for which to search.

Returns:

The string from the initial position through the end of the terminating sequence, or through the end of the stream if no terminating sequence is found.

Throws:

java.io.IOException

findString

public java.lang.String findString(boolean saveString,
                          java.lang.String... terminators)
                            throws java.io.IOException

Reads or skips a string ending with one of the given terminating substrings.

Parameters:

saveString - Whether to collect the string from the current file pointer to the terminating bytes, and return it. If false, returns null.

terminators - The strings for which to search.

Returns:

The string from the initial position through the end of the terminating sequence, or through the end of the stream if no terminating sequence is found, or null if saveString flag is unset.

Throws:

java.io.IOException - If saveString flag is set and the maximum search length (512 MB) is exceeded.

findString

public java.lang.String findString(int blockSize,
                          java.lang.String... terminators)
                            throws java.io.IOException

Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.

Parameters:

blockSize - The block size to use when reading bytes in chunks.

terminators - The strings for which to search.

Returns:

The string from the initial position through the end of the terminating sequence, or through the end of the stream if no terminating sequence is found.

Throws:

java.io.IOException

findString

public java.lang.String findString(boolean saveString,
                          int blockSize,
                          java.lang.String... terminators)
                            throws java.io.IOException

Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.

Parameters:

saveString - Whether to collect the string from the current file pointer to the terminating bytes, and return it. If false, returns null.

blockSize - The block size to use when reading bytes in chunks.

terminators - The strings for which to search.

Returns:

The string from the initial position through the end of the terminating sequence, or through the end of the stream if no terminating sequence is found, or null if saveString flag is unset.

Throws:

java.io.IOException - If saveString flag is set and the maximum search length (512 MB) is exceeded.

readBoolean

public boolean readBoolean()
                    throws java.io.IOException

Read an input byte and return true if the byte is nonzero.

Specified by:

readBoolean in interface java.io.DataInput

Throws:

java.io.IOException

readByte

public byte readByte()
              throws java.io.IOException

Read one byte and return it.

Specified by:

readByte in interface java.io.DataInput

Throws:

java.io.IOException

readChar

public char readChar()
              throws java.io.IOException

Read an input char.

Specified by:

readChar in interface java.io.DataInput

Throws:

java.io.IOException

readDouble

public double readDouble()
                  throws java.io.IOException

Read eight bytes and return a double value.

Specified by:

readDouble in interface java.io.DataInput

Throws:

java.io.IOException

readFloat

public float readFloat()
                throws java.io.IOException

Read four bytes and return a float value.

Specified by:

readFloat in interface java.io.DataInput

Throws:

java.io.IOException

readInt

public int readInt()
            throws java.io.IOException

Read four input bytes and return an int value.

Specified by:

readInt in interface java.io.DataInput

Throws:

java.io.IOException

readLine

public java.lang.String readLine()
                          throws java.io.IOException

Read the next line of text from the input stream.

Specified by:

readLine in interface java.io.DataInput

Throws:

java.io.IOException

readCString

public java.lang.String readCString()
                             throws java.io.IOException

Read a string of arbitrary length, terminated by a null char.

Throws:

java.io.IOException

readString

public java.lang.String readString(int n)
                            throws java.io.IOException

Read a string of up to length n.

Throws:

java.io.IOException

readLong

public long readLong()
              throws java.io.IOException

Read eight input bytes and return a long value.

Specified by:

readLong in interface java.io.DataInput

Throws:

java.io.IOException

readShort

public short readShort()
                throws java.io.IOException

Read two input bytes and return a short value.

Specified by:

readShort in interface java.io.DataInput

Throws:

java.io.IOException

readUnsignedByte

public int readUnsignedByte()
                     throws java.io.IOException

Read an input byte and zero extend it appropriately.

Specified by:

readUnsignedByte in interface java.io.DataInput

Throws:

java.io.IOException

readUnsignedShort

public int readUnsignedShort()
                      throws java.io.IOException

Read two bytes and return an int in the range 0 through 65535.

Specified by:

readUnsignedShort in interface java.io.DataInput

Throws:

java.io.IOException

readUTF

public java.lang.String readUTF()
                         throws java.io.IOException

Read a string that has been encoded using a modified UTF-8 format.

Specified by:

readUTF in interface java.io.DataInput

Throws:

java.io.IOException

skipBytes

public int skipBytes(int n)
              throws java.io.IOException

Skip n bytes within the stream.

Specified by:

skipBytes in interface java.io.DataInput

Throws:

java.io.IOException

read

public int read(byte[] array)
         throws java.io.IOException

Read bytes from the stream into the given array.

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] array,
       int offset,
       int n)
         throws java.io.IOException

Read n bytes from the stream into the given array at the specified offset.

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(java.nio.ByteBuffer buf)
         throws java.io.IOException

Read bytes from the stream into the given buffer.

Throws:

java.io.IOException

read

public int read(java.nio.ByteBuffer buf,
       int offset,
       int n)
         throws java.io.IOException

Read n bytes from the stream into the given buffer at the specified offset.

Throws:

java.io.IOException

readFully

public void readFully(byte[] array)
               throws java.io.IOException

Read bytes from the stream into the given array.

Specified by:

readFully in interface java.io.DataInput

Throws:

java.io.IOException

readFully

public void readFully(byte[] array,
             int offset,
             int n)
               throws java.io.IOException

Read n bytes from the stream into the given array at the specified offset.

Specified by:

readFully in interface java.io.DataInput

Throws:

java.io.IOException

read

public int read()
         throws java.io.IOException

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

available

public int available()
              throws java.io.IOException

Overrides:

available in class java.io.InputStream

Throws:

java.io.IOException

mark

public void mark(int readLimit)

Overrides:

mark in class java.io.InputStream

markSupported

public boolean markSupported()

Overrides:

markSupported in class java.io.InputStream

reset

public void reset()
           throws java.io.IOException

Overrides:

reset in class java.io.InputStream

Throws:

java.io.IOException

read

public void read(com.esotericsoftware.kryo.Kryo kryo,
        com.esotericsoftware.kryo.io.Input in)

Specified by:

read in interface com.esotericsoftware.kryo.KryoSerializable

write

public void write(com.esotericsoftware.kryo.Kryo kryo,
         com.esotericsoftware.kryo.io.Output out)

Specified by:

write in interface com.esotericsoftware.kryo.KryoSerializable