Package loci.common

Class NIOInputStream

java.lang.Object
java.io.InputStream
loci.common.NIOInputStream
All Implemented Interfaces:
java.io.Closeable, java.io.DataInput, java.lang.AutoCloseable
public class NIOInputStream
extends java.io.InputStream
implements java.io.DataInput
NIOInputStream provides methods for "intelligent" reading of files and byte arrays.

  • Field Summary

    Fields 
    Modifier and Type Field Description
    protected java.nio.channels.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 java.io.File file
    The file.
    protected java.lang.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 Description
    NIOInputStream​(byte[] array)
    Constructs a random access stream around the given byte array.
    NIOInputStream​(java.lang.String filename)
    Constructs an NIOInputStream around the given file.
    NIOInputStream​(IRandomAccess handle)
    Constructs a random access stream around the given handle.

  • Method Summary

    Modifier and Type Method 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()  
    java.io.DataInputStream getInputStream()  
    boolean isLittleEndian()  
    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.
    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 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 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

    nullInputStream, readAllBytes, readNBytes, readNBytes, skip, skipNBytes, transferTo

    Methods inherited from class java.lang.Object

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

  • Field Details

    • 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 java.lang.String filename
      The file name.

    • file

      protected java.io.File file
      The file.

    • channel

      protected java.nio.channels.Channel channel
      The file channel backed by the random access file.

    • isLittleEndian

      protected boolean isLittleEndian
      Endianness of the stream.

  • Constructor Details

    • NIOInputStream

      public NIOInputStream​(java.lang.String filename) throws java.io.IOException
      Constructs an NIOInputStream around the given file.
      Parameters:
      filename - the path to a readable file on disk
      Throws:
      java.io.IOException - if the path is invalid or unreadable

    • NIOInputStream

      public NIOInputStream​(IRandomAccess handle)
      Constructs a random access stream around the given handle.
      Parameters:
      handle - the IRandomAccess to wrap in a stream

    • NIOInputStream

      public NIOInputStream​(byte[] array)
      Constructs a random access stream around the given byte array.
      Parameters:
      array - the byte array to wrap in a stream

  • Method Details

    • getInputStream

      public java.io.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.
      Parameters:
      extend - the number of bytes by which to extend the stream

    • seek

      public void seek​(long pos) throws java.io.IOException
      Seeks to the given offset within the stream.
      Parameters:
      pos - the offset to which to seek
      Throws:
      java.io.IOException - if the seek is not successful

    • read

      public int read() throws java.io.IOException
      Alias for readByte().
      Specified by:
      read in class java.io.InputStream
      Throws:
      java.io.IOException

    • length

      public long length() throws java.io.IOException
      Gets the number of bytes in the file.
      Returns:
      the length of the stream in bytes
      Throws:
      java.io.IOException - if the length cannot be retrieved

    • getFilePointer

      public long getFilePointer()
      Returns:
      the current (absolute) file pointer.

    • close

      public void close() throws java.io.IOException
      Closes the streams.
      Specified by:
      close in interface java.lang.AutoCloseable
      Specified by:
      close in interface java.io.Closeable
      Overrides:
      close in class java.io.InputStream
      Throws:
      java.io.IOException

    • order

      public void order​(boolean isLittleEndian)
      Sets the endianness of the stream.
      Parameters:
      isLittleEndian - true if the stream order is little-endian

    • isLittleEndian

      public boolean isLittleEndian()
      Returns:
      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.
      Parameters:
      lastChars - string containing possible final characters for the returned string
      Returns:
      the smallest string that ends in one of the characters in lastChars
      Throws:
      java.io.IOException - If the maximum length (512 MB) is exceeded.
      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 - If the maximum search length (512 MB) is exceeded.

    • 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.
      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 - If the maximum search length (512 MB) is exceeded.

    • 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.
      Returns:
      the smallest string such that the last character is a null byte
      Throws:
      java.io.IOException - if a null-terminated string is not found
      See Also:
      findString(String...)

    • readString

      public java.lang.String readString​(int n) throws java.io.IOException
      Read a string of length n.
      Parameters:
      n - the number of bytes to read
      Returns:
      a string representing the next n bytes in the stream
      Throws:
      java.io.IOException - if there is an error during reading

    • 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

    • 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

    • 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