NIOInputStream (Bio-Formats API)

java.lang.Object
- java.io.InputStream
- - loci.common.NIOInputStream

All Implemented Interfaces:

Closeable, DataInput, AutoCloseable
```
public class NIOInputStream
extends InputStream
implements DataInput
```
NIOInputStream provides methods for "intelligent" reading of files and byte arrays.

Field Summary

Fields
Modifier and Type	Field and Description
`protected Channel`	`channel` The file channel backed by the random access file.
`protected static int`	`DEFAULT_BLOCK_SIZE` Block size to use when searching through the stream.
`protected File`	`file` The file.
`protected String`	`filename` The file name.
`protected boolean`	`isLittleEndian` Endianness of the stream.
`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
`NIOInputStream(byte[] array)` Constructs a random access stream around the given byte array.
`NIOInputStream(IRandomAccess handle)` Constructs a random access stream around the given handle.
`NIOInputStream(String filename)` Constructs an NIOInputStream around the given file.

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`available()`
`void`	`close()` Closes the streams.
`String`	`findString(boolean saveString, int blockSize, String... terminators)` Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
`String`	`findString(boolean saveString, String... terminators)` Reads or skips a string ending with one of the given terminating substrings.
`String`	`findString(int blockSize, String... terminators)` Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
`String`	`findString(String... terminators)` Reads a string ending with one of the given terminating substrings.
`long`	`getFilePointer()` Gets the current (absolute) file pointer.
`DataInputStream`	`getInputStream()` Returns the underlying InputStream.
`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 isLittleEndian)` Sets the endianness of the stream.
`int`	`read()` Alias for readByte().
`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.
`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.
`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.
`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.
`String`	`readString(int n)` Read a string of length n.
`String`	`readString(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.
`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`	`setExtend(int extend)` Sets the number of bytes by which to extend the stream.
`int`	`skipBytes(int n)` Skip n bytes within the stream.

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
  - DEFAULT_BLOCK_SIZE
```
protected static final int DEFAULT_BLOCK_SIZE
```
    Block size to use when searching through the stream. This value should not exceed MAX_OVERHEAD!
    
    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
```
  - filename
```
protected String filename
```
    The file name.
  - file
```
protected File file
```
    The file.
  - channel
```
protected Channel channel
```
    The file channel backed by the random access file.
  - isLittleEndian
```
protected boolean isLittleEndian
```
    Endianness of the stream.
- Constructor Detail
  - NIOInputStream
```
public NIOInputStream(String filename)
               throws IOException
```
    Constructs an NIOInputStream around the given file.
    
    Throws:
    
    IOException
  - NIOInputStream
```
public NIOInputStream(IRandomAccess handle)
```
    Constructs a random access stream around the given handle.
  - NIOInputStream
```
public NIOInputStream(byte[] array)
```
    Constructs a random access stream around the given byte array.
- Method Detail
  - getInputStream
```
public DataInputStream getInputStream()
```
    Returns the underlying InputStream.
  - setExtend
```
public void setExtend(int extend)
```
    Sets the number of bytes by which to extend the stream. This only applies to InputStream API methods.
  - seek
```
public void seek(long pos)
          throws IOException
```
    Seeks to the given offset within the stream.
    
    Throws:
    
    IOException
  - read
```
public int read()
         throws IOException
```
    Alias for readByte().
    
    Specified by:
    
    read in class InputStream
    
    Throws:
    
    IOException
  - length
```
public long length()
            throws IOException
```
    Gets the number of bytes in the file.
    
    Throws:
    
    IOException
  - getFilePointer
```
public long getFilePointer()
```
    Gets the current (absolute) file pointer.
  - close
```
public void close()
           throws IOException
```
    Closes the streams.
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
    
    Overrides:
    
    close in class InputStream
    
    Throws:
    
    IOException
  - order
```
public void order(boolean isLittleEndian)
```
    Sets the endianness of the stream.
  - isLittleEndian
```
public boolean isLittleEndian()
```
    Gets the endianness of the stream.
  - readString
```
public String readString(String lastChars)
                  throws IOException
```
    Reads a string ending with one of the characters in the given string.
    
    Throws:
    
    IOException
    See Also:
    findString(String...)
  - findString
```
public String findString(String... terminators)
                  throws 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:
    
    IOException
  - findString
```
public String findString(boolean saveString,
                String... terminators)
                  throws 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:
    
    IOException - If saveString flag is set and the maximum search length (512 MB) is exceeded.
  - findString
```
public String findString(int blockSize,
                String... terminators)
                  throws 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:
    
    IOException
  - findString
```
public String findString(boolean saveString,
                int blockSize,
                String... terminators)
                  throws 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:
    
    IOException - If saveString flag is set and the maximum search length (512 MB) is exceeded.
  - readBoolean
```
public boolean readBoolean()
                    throws IOException
```
    Read an input byte and return true if the byte is nonzero.
    
    Specified by:
    
    readBoolean in interface DataInput
    
    Throws:
    
    IOException
  - readByte
```
public byte readByte()
              throws IOException
```
    Read one byte and return it.
    
    Specified by:
    
    readByte in interface DataInput
    
    Throws:
    
    IOException
  - readChar
```
public char readChar()
              throws IOException
```
    Read an input char.
    
    Specified by:
    
    readChar in interface DataInput
    
    Throws:
    
    IOException
  - readDouble
```
public double readDouble()
                  throws IOException
```
    Read eight bytes and return a double value.
    
    Specified by:
    
    readDouble in interface DataInput
    
    Throws:
    
    IOException
  - readFloat
```
public float readFloat()
                throws IOException
```
    Read four bytes and return a float value.
    
    Specified by:
    
    readFloat in interface DataInput
    
    Throws:
    
    IOException
  - readInt
```
public int readInt()
            throws IOException
```
    Read four input bytes and return an int value.
    
    Specified by:
    
    readInt in interface DataInput
    
    Throws:
    
    IOException
  - readLine
```
public String readLine()
                throws IOException
```
    Read the next line of text from the input stream.
    
    Specified by:
    
    readLine in interface DataInput
    
    Throws:
    
    IOException
  - readCString
```
public String readCString()
                   throws IOException
```
    Read a string of arbitrary length, terminated by a null char.
    
    Throws:
    
    IOException
  - readString
```
public String readString(int n)
                  throws IOException
```
    Read a string of length n.
    
    Throws:
    
    IOException
  - readLong
```
public long readLong()
              throws IOException
```
    Read eight input bytes and return a long value.
    
    Specified by:
    
    readLong in interface DataInput
    
    Throws:
    
    IOException
  - readShort
```
public short readShort()
                throws IOException
```
    Read two input bytes and return a short value.
    
    Specified by:
    
    readShort in interface DataInput
    
    Throws:
    
    IOException
  - readUnsignedByte
```
public int readUnsignedByte()
                     throws IOException
```
    Read an input byte and zero extend it appropriately.
    
    Specified by:
    
    readUnsignedByte in interface DataInput
    
    Throws:
    
    IOException
  - readUnsignedShort
```
public int readUnsignedShort()
                      throws IOException
```
    Read two bytes and return an int in the range 0 through 65535.
    
    Specified by:
    
    readUnsignedShort in interface DataInput
    
    Throws:
    
    IOException
  - readUTF
```
public String readUTF()
               throws IOException
```
    Read a string that has been encoded using a modified UTF-8 format.
    
    Specified by:
    
    readUTF in interface DataInput
    
    Throws:
    
    IOException
  - skipBytes
```
public int skipBytes(int n)
              throws IOException
```
    Skip n bytes within the stream.
    
    Specified by:
    
    skipBytes in interface DataInput
    
    Throws:
    
    IOException
  - read
```
public int read(byte[] array)
         throws IOException
```
    Read bytes from the stream into the given array.
    
    Overrides:
    
    read in class InputStream
    
    Throws:
    
    IOException
  - read
```
public int read(byte[] array,
       int offset,
       int n)
         throws IOException
```
    Read n bytes from the stream into the given array at the specified offset.
    
    Overrides:
    
    read in class InputStream
    
    Throws:
    
    IOException
  - readFully
```
public void readFully(byte[] array)
               throws IOException
```
    Read bytes from the stream into the given array.
    
    Specified by:
    
    readFully in interface DataInput
    
    Throws:
    
    IOException
  - readFully
```
public void readFully(byte[] array,
             int offset,
             int n)
               throws IOException
```
    Read n bytes from the stream into the given array at the specified offset.
    
    Specified by:
    
    readFully in interface DataInput
    
    Throws:
    
    IOException
  - available
```
public int available()
              throws IOException
```
    Overrides:
    
    available in class InputStream
    
    Throws:
    
    IOException
  - mark
```
public void mark(int readLimit)
```
    Overrides:
    
    mark in class InputStream
  - markSupported
```
public boolean markSupported()
```
    Overrides:
    
    markSupported in class InputStream
  - reset
```
public void reset()
           throws IOException
```
    Overrides:
    
    reset in class InputStream
    
    Throws:
    
    IOException

Class NIOInputStream

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.io.InputStream

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_BLOCK_SIZE

MAX_SEARCH_SIZE

raf

filename

file

channel

isLittleEndian

Constructor Detail

NIOInputStream

NIOInputStream

NIOInputStream

Method Detail

getInputStream

setExtend

seek

read

length

getFilePointer

close

order

isLittleEndian

readString

findString

findString

findString

findString

readBoolean

readByte

readChar

readDouble

readFloat

readInt

readLine

readCString

readString

readLong

readShort

readUnsignedByte

readUnsignedShort

readUTF

skipBytes

read

read

readFully

readFully

available

mark

markSupported

reset