Package loci.common

Class ByteArrayHandle

java.lang.Object
loci.common.AbstractNIOHandle
loci.common.ByteArrayHandle
All Implemented Interfaces:
java.io.DataInput, java.io.DataOutput, IRandomAccess
public class ByteArrayHandle
extends AbstractNIOHandle
A wrapper for a byte array that implements the IRandomAccess interface.
See Also:
IRandomAccess

  • Field Summary

    Fields 
    Modifier and Type Field Description
    protected java.nio.ByteBuffer buffer
    Backing ByteBuffer.
    protected static int INITIAL_LENGTH
    Initial length of a new file.

    Fields inherited from class loci.common.AbstractNIOHandle

    EOF_ERROR_MSG

  • Constructor Summary

    Constructors 
    Constructor Description
    ByteArrayHandle()
    Creates a random access byte stream to write to a byte array.
    ByteArrayHandle​(byte[] bytes)
    Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
    ByteArrayHandle​(int capacity)
    Creates a random access byte stream to read from, and write to.
    ByteArrayHandle​(java.nio.ByteBuffer bytes)
    Creates a random access byte stream to read from, and write to, the supplied ByteBuffer.

  • Method Summary

    Modifier and Type Method Description
    void close()
    Closes this random access stream and releases any system resources associated with the stream.
    java.nio.ByteBuffer getByteBuffer()
    Gets the byte buffer backing this handle.
    byte[] getBytes()
    Gets a byte array representing the current state of this ByteArrayHandle.
    long getFilePointer()
    Returns the current offset in this stream.
    java.nio.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​(java.nio.ByteBuffer buf)
    Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
    int read​(java.nio.ByteBuffer buf, 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()  
    java.lang.String readLine()  
    long readLong()  
    short readShort()  
    int readUnsignedByte()  
    int readUnsignedShort()  
    java.lang.String readUTF()  
    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 setLength​(long length)
    Sets the new length of the handle.
    void setOrder​(java.nio.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​(int b)  
    void write​(java.nio.ByteBuffer buf)
    Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
    void write​(java.nio.ByteBuffer buf, int off, int len)
    Writes up to len bytes of data from the given ByteBuffer to this stream.
    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 loci.common.AbstractNIOHandle

    exists, validateLength, validateMode

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • ByteArrayHandle

      public ByteArrayHandle​(byte[] bytes)
      Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
      Parameters:
      bytes - byte array to work with

    • ByteArrayHandle

      public ByteArrayHandle​(java.nio.ByteBuffer bytes)
      Creates a random access byte stream to read from, and write to, the supplied ByteBuffer.
      Parameters:
      bytes - ByteBuffer used for reading and writing

    • ByteArrayHandle

      public ByteArrayHandle​(int capacity)
      Creates a random access byte stream to read from, and write to.
      Parameters:
      capacity - Number of bytes to initially allocate.

    • ByteArrayHandle

      public ByteArrayHandle()
      Creates a random access byte stream to write to a byte array.

  • Method Details

    • getBytes

      public byte[] getBytes()
      Gets a byte array representing the current state of this ByteArrayHandle.
      Returns:
      a byte array representation of the backing ByteBuffer

    • getByteBuffer

      public java.nio.ByteBuffer getByteBuffer()
      Gets the byte buffer backing this handle. NOTE: This is the backing buffer. Any modifications to this buffer including position, length and capacity will affect subsequent calls upon its source handle.
      Returns:
      Backing buffer of this handle.

    • setLength

      public void setLength​(long length) throws java.io.IOException
      Description copied from class: AbstractNIOHandle
      Sets the new length of the handle.
      Specified by:
      setLength in class AbstractNIOHandle
      Parameters:
      length - New length.
      Throws:
      java.io.IOException - If there is an error changing the handle's length.

    • close

      public void close()
      Description copied from interface: IRandomAccess
      Closes this random access stream and releases any system resources associated with the stream.

    • getFilePointer

      public long getFilePointer()
      Description copied from interface: IRandomAccess
      Returns the current offset in this stream.
      Returns:
      the current byte offset within the file; expected to be non-negative and less than the value of #length()

    • length

      public long length()
      Description copied from interface: IRandomAccess
      Returns the length of this stream.
      Returns:
      the length in bytes of the stream

    • read

      public int read​(byte[] b) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Reads up to b.length bytes of data from this stream into an array of bytes.
      Parameters:
      b - the array to fill from this stream
      Returns:
      the total number of bytes read into the buffer.
      Throws:
      java.io.IOException - if reading is not possible

    • read

      public int read​(byte[] b, int off, int len) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Reads up to len bytes of data from this stream into an array of bytes.
      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:
      java.io.IOException - if reading is not possible

    • read

      public int read​(java.nio.ByteBuffer buf) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
      Parameters:
      buf - the ByteBuffer to fill from this stream
      Returns:
      the total number of bytes read into the buffer.
      Throws:
      java.io.IOException - if reading is not possible

    • read

      public int read​(java.nio.ByteBuffer buf, int off, int len) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Reads up to len bytes of data from this stream into a ByteBuffer.
      Parameters:
      buf - 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:
      java.io.IOException - if reading is not possible

    • seek

      public void seek​(long pos) throws java.io.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.
      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:
      java.io.IOException - if pos is invalid or the seek fails
      See Also:
      IRandomAccess.getFilePointer()

    • getOrder

      public java.nio.ByteOrder getOrder()
      Description copied from interface: IRandomAccess
      Returns the current order (endianness) of the stream.
      Returns:
      See above.

    • setOrder

      public void setOrder​(java.nio.ByteOrder order)
      Description copied from interface: IRandomAccess
      Sets the byte order (endianness) of the stream.
      Parameters:
      order - Order to set.

    • readBoolean

      public boolean readBoolean() throws java.io.IOException
      Throws:
      java.io.IOException

    • readByte

      public byte readByte() throws java.io.IOException
      Throws:
      java.io.IOException

    • readChar

      public char readChar() throws java.io.IOException
      Throws:
      java.io.IOException

    • readDouble

      public double readDouble() throws java.io.IOException
      Throws:
      java.io.IOException

    • readFloat

      public float readFloat() throws java.io.IOException
      Throws:
      java.io.IOException

    • readFully

      public void readFully​(byte[] b) throws java.io.IOException
      Throws:
      java.io.IOException

    • readFully

      public void readFully​(byte[] b, int off, int len) throws java.io.IOException
      Throws:
      java.io.IOException

    • readInt

      public int readInt() throws java.io.IOException
      Throws:
      java.io.IOException

    • readLine

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

    • readLong

      public long readLong() throws java.io.IOException
      Throws:
      java.io.IOException

    • readShort

      public short readShort() throws java.io.IOException
      Throws:
      java.io.IOException

    • readUnsignedByte

      public int readUnsignedByte() throws java.io.IOException
      Throws:
      java.io.IOException

    • readUnsignedShort

      public int readUnsignedShort() throws java.io.IOException
      Throws:
      java.io.IOException

    • readUTF

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

    • skipBytes

      public int skipBytes​(int n) throws java.io.IOException
      Throws:
      java.io.IOException

    • skipBytes

      public long skipBytes​(long n) throws java.io.IOException
      Description copied from interface: IRandomAccess
      A long variant of DataInput.skipBytes(int).
      Parameters:
      n - the number of bytes to skip
      Returns:
      the number of bytes skipped
      Throws:
      java.io.IOException - if the operation failed

    • write

      public void write​(byte[] b) throws java.io.IOException
      Throws:
      java.io.IOException

    • write

      public void write​(byte[] b, int off, int len) throws java.io.IOException
      Throws:
      java.io.IOException

    • write

      public void write​(java.nio.ByteBuffer buf) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
      Parameters:
      buf - the ByteBuffer containing bytes to write to this stream
      Throws:
      java.io.IOException - if writing is not possible

    • write

      public void write​(java.nio.ByteBuffer buf, int off, int len) throws java.io.IOException
      Description copied from interface: IRandomAccess
      Writes up to len bytes of data from the given ByteBuffer to this stream.
      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:
      java.io.IOException - if writing is not possible

    • write

      public void write​(int b) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeBoolean

      public void writeBoolean​(boolean v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeByte

      public void writeByte​(int v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeBytes

      public void writeBytes​(java.lang.String s) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeChar

      public void writeChar​(int v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeChars

      public void writeChars​(java.lang.String s) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeDouble

      public void writeDouble​(double v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeFloat

      public void writeFloat​(float v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeInt

      public void writeInt​(int v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeLong

      public void writeLong​(long v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeShort

      public void writeShort​(int v) throws java.io.IOException
      Throws:
      java.io.IOException

    • writeUTF

      public void writeUTF​(java.lang.String str) throws java.io.IOException
      Throws:
      java.io.IOException