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        IOUtils (Commons IO 2.4 API)
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        org.apache.commons.io

    Class IOUtils

java.lang.Object
  org.apache.commons.io.IOUtils

public class IOUtils
extends Object

    General IO stream manipulation utilities.

    This class provides static utility methods for input/output operations.

closeQuietly - these methods close a stream ignoring nulls and exceptions

toXxx/read - these methods read data from a stream

write - these methods write data to a stream

copy - these methods copy all the data from one stream to another

contentEquals - these methods compare the content of two streams

    The byte-to-char methods and char-to-byte methods involve a conversion step.
    Two methods are provided in each case, one that uses the platform default
    encoding and the other which allows you to specify an encoding. You are
    encouraged to always specify an encoding because relying on the platform
    default can lead to unexpected results, for example when moving from
    development to production.

    All the methods in this class that read a stream are buffered internally.
    This means that there is no cause to use a BufferedInputStream
    or BufferedReader. The default buffer size of 4K has been shown
    to be efficient in tests.

    Wherever possible, the methods in this class do not flush or close
    the stream. This is to avoid making non-portable assumptions about the
    streams' origin and further use. Thus the caller is still responsible for
    closing streams after use.

    Origin of code: Excalibur.

Version:

$Id: IOUtils.java 1326636 2012-04-16 14:54:53Z ggregory $

            Field Summary

            static char
        DIR_SEPARATOR

                      The system directory separator character.

            static char
        DIR_SEPARATOR_UNIX

                      The Unix directory separator character.

            static char
        DIR_SEPARATOR_WINDOWS

                      The Windows directory separator character.

            static String
        LINE_SEPARATOR

                      The system line separator string.

            static String
        LINE_SEPARATOR_UNIX

                      The Unix line separator string.

            static String
        LINE_SEPARATOR_WINDOWS

                      The Windows line separator string.

            Constructor Summary

        IOUtils()

                      Instances should NOT be constructed in standard
            programming.

            Method Summary

            static void
        close(URLConnection conn)

                      Closes a URLConnection.

            static void
        closeQuietly(Closeable closeable)

                      Unconditionally close a Closeable.

            static void
        closeQuietly(InputStream input)

                      Unconditionally close an
            InputStream.

            static void
        closeQuietly(OutputStream output)

                      Unconditionally close an
            OutputStream.

            static void
        closeQuietly(Reader input)

                      Unconditionally close an Reader.

            static void
        closeQuietly(Selector selector)

                      Unconditionally close a Selector.

            static void
        closeQuietly(ServerSocket sock)

                      Unconditionally close a
            ServerSocket.

            static void
        closeQuietly(Socket sock)

                      Unconditionally close a Socket.

            static void
        closeQuietly(Writer output)

                      Unconditionally close a Writer.

            static boolean
        contentEquals(InputStream input1,
            InputStream input2)

                      Compare the contents of two Streams to determine
            if they are equal or
            not.

            static boolean
        contentEquals(Reader input1,
            Reader input2)

                      Compare the contents of two Readers to determine
            if they are equal or
            not.

            static boolean
        contentEqualsIgnoreEOL(Reader input1,
            Reader input2)

                      Compare the contents of two Readers to determine
            if they are equal or
            not, ignoring EOL characters.

            static int
        copy(InputStream input,
            OutputStream output)

                      Copy bytes from an InputStream to
            an
            OutputStream.

            static void
        copy(InputStream input,
            Writer output)

                      Copy bytes from an InputStream to
            chars on a
            Writer using the default character encoding of the platform.

            static void
        copy(InputStream input,
            Writer output,
            Charset encoding)

                      Copy bytes from an InputStream to
            chars on a
            Writer using the specified character encoding.

            static void
        copy(InputStream input,
            Writer output,
            String encoding)

                      Copy bytes from an InputStream to
            chars on a
            Writer using the specified character encoding.

            static void
        copy(Reader input,
            OutputStream output)

                      Copy chars from a Reader to bytes
            on an
            OutputStream using the default character encoding of the
            platform, and calling flush.

            static void
        copy(Reader input,
            OutputStream output,
            Charset encoding)

                      Copy chars from a Reader to bytes
            on an
            OutputStream using the specified character encoding, and
            calling flush.

            static void
        copy(Reader input,
            OutputStream output,
            String encoding)

                      Copy chars from a Reader to bytes
            on an
            OutputStream using the specified character encoding, and
            calling flush.

            static int
        copy(Reader input,
            Writer output)

                      Copy chars from a Reader to a
            Writer.

            static long
        copyLarge(InputStream input,
            OutputStream output)

                      Copy bytes from a large (over 2GB) InputStream
            to an
            OutputStream.

            static long
        copyLarge(InputStream input,
            OutputStream output,
            byte[] buffer)

                      Copy bytes from a large (over 2GB) InputStream
            to an
            OutputStream.

            static long
        copyLarge(InputStream input,
            OutputStream output,
            long inputOffset,
            long length)

                      Copy some or all bytes from a large (over 2GB)
            InputStream to an
            OutputStream, optionally skipping input bytes.

            static long
        copyLarge(InputStream input,
            OutputStream output,
            long inputOffset,
            long length,
            byte[] buffer)

                      Copy some or all bytes from a large (over 2GB)
            InputStream to an
            OutputStream, optionally skipping input bytes.

            static long
        copyLarge(Reader input,
            Writer output)

                      Copy chars from a large (over 2GB)
            Reader to a Writer.

            static long
        copyLarge(Reader input,
            Writer output,
            char[] buffer)

                      Copy chars from a large (over 2GB)
            Reader to a Writer.

            static long
        copyLarge(Reader input,
            Writer output,
            long inputOffset,
            long length)

                      Copy some or all chars from a large (over 2GB)
            InputStream to an
            OutputStream, optionally skipping input chars.

            static long
        copyLarge(Reader input,
            Writer output,
            long inputOffset,
            long length,
            char[] buffer)

                      Copy some or all chars from a large (over 2GB)
            InputStream to an
            OutputStream, optionally skipping input chars.

            static LineIterator
        lineIterator(InputStream input,
            Charset encoding)

                      Return an Iterator for the lines in an InputStream,
            using
            the character encoding specified (or default encoding if null).

            static LineIterator
        lineIterator(InputStream input,
            String encoding)

                      Return an Iterator for the lines in an InputStream,
            using
            the character encoding specified (or default encoding if null).

            static LineIterator
        lineIterator(Reader reader)

                      Return an Iterator for the lines in a Reader.

            static int
        read(InputStream input,
            byte[] buffer)

                      Read bytes from an input stream.

            static int
        read(InputStream input,
            byte[] buffer,
            int offset,
            int length)

                      Read bytes from an input stream.

            static int
        read(Reader input,
            char[] buffer)

                      Read characters from an input character stream.

            static int
        read(Reader input,
            char[] buffer,
            int offset,
            int length)

                      Read characters from an input character stream.

            static void
        readFully(InputStream input,
            byte[] buffer)

                      Read the requested number of bytes or fail if
            there are not enough left.

            static void
        readFully(InputStream input,
            byte[] buffer,
            int offset,
            int length)

                      Read the requested number of bytes or fail if
            there are not enough left.

            static void
        readFully(Reader input,
            char[] buffer)

                      Read the requested number of characters or fail
            if there are not enough left.

            static void
        readFully(Reader input,
            char[] buffer,
            int offset,
            int length)

                      Read the requested number of characters or fail
            if there are not enough left.

            static List<String>
        readLines(InputStream input)

                      Get the contents of an InputStream
            as a list of Strings,
            one entry per line, using the default character encoding of the platform.

            static List<String>
        readLines(InputStream input,
            Charset encoding)

                      Get the contents of an InputStream
            as a list of Strings,
            one entry per line, using the specified character encoding.

            static List<String>
        readLines(InputStream input,
            String encoding)

                      Get the contents of an InputStream
            as a list of Strings,
            one entry per line, using the specified character encoding.

            static List<String>
        readLines(Reader input)

                      Get the contents of a Reader as a
            list of Strings,
            one entry per line.

            static long
        skip(InputStream input,
            long toSkip)

                      Skip bytes from an input byte stream.

            static long
        skip(Reader input,
            long toSkip)

                      Skip characters from an input character stream.

            static void
        skipFully(InputStream input,
            long toSkip)

                      Skip the requested number of bytes or fail if
            there are not enough left.

            static void
        skipFully(Reader input,
            long toSkip)

                      Skip the requested number of characters or fail
            if there are not enough left.

            static InputStream
        toBufferedInputStream(InputStream input)

                      Fetches entire contents of an
            InputStream and represent
            same data as result InputStream.

            static BufferedReader
        toBufferedReader(Reader reader)

                      Returns the given reader if it is a BufferedReader, otherwise creates a
            toBufferedReader for the given
            reader.

            static byte[]
        toByteArray(InputStream input)

                      Get the contents of an InputStream
            as a byte[].

            static byte[]
        toByteArray(InputStream input,
            int size)

                      Get the contents of an InputStream
            as a byte[].

            static byte[]
        toByteArray(InputStream input,
            long size)

                      Get contents of an InputStream as a
            byte[].

            static byte[]
        toByteArray(Reader input)

                      Get the contents of a Reader as a
            byte[]
            using the default character encoding of the platform.

            static byte[]
        toByteArray(Reader input,
            Charset encoding)

                      Get the contents of a Reader as a
            byte[]
            using the specified character encoding.

            static byte[]
        toByteArray(Reader input,
            String encoding)

                      Get the contents of a Reader as a
            byte[]
            using the specified character encoding.

            static byte[]
        toByteArray(String input)

                      Deprecated. Use String.getBytes()

            static byte[]
        toByteArray(URI uri)

                      Get the contents of a URI as a
            byte[].

            static byte[]
        toByteArray(URL url)

                      Get the contents of a URL as a
            byte[].

            static byte[]
        toByteArray(URLConnection urlConn)

                      Get the contents of a URLConnection
            as a byte[].

            static char[]
        toCharArray(InputStream is)

                      Get the contents of an InputStream
            as a character array
            using the default character encoding of the platform.

            static char[]
        toCharArray(InputStream is,
            Charset encoding)

                      Get the contents of an InputStream
            as a character array
            using the specified character encoding.

            static char[]
        toCharArray(InputStream is,
            String encoding)

                      Get the contents of an InputStream
            as a character array
            using the specified character encoding.

            static char[]
        toCharArray(Reader input)

                      Get the contents of a Reader as a
            character array.

            static InputStream
        toInputStream(CharSequence input)

                      Convert the specified CharSequence to an input
            stream, encoded as bytes
            using the default character encoding of the platform.

            static InputStream
        toInputStream(CharSequence input,
            Charset encoding)

                      Convert the specified CharSequence to an input
            stream, encoded as bytes
            using the specified character encoding.

            static InputStream
        toInputStream(CharSequence input,
            String encoding)

                      Convert the specified CharSequence to an input
            stream, encoded as bytes
            using the specified character encoding.

            static InputStream
        toInputStream(String input)

                      Convert the specified string to an input stream,
            encoded as bytes
            using the default character encoding of the platform.

            static InputStream
        toInputStream(String input,
            Charset encoding)

                      Convert the specified string to an input stream,
            encoded as bytes
            using the specified character encoding.

            static InputStream
        toInputStream(String input,
            String encoding)

                      Convert the specified string to an input stream,
            encoded as bytes
            using the specified character encoding.

            static String
        toString(byte[] input)

                      Deprecated. Use String.String(byte[])

            static String
        toString(byte[] input,
            String encoding)

                      Get the contents of a byte[] as a
            String
            using the specified character encoding.

            static String
        toString(InputStream input)

                      Get the contents of an InputStream
            as a String
            using the default character encoding of the platform.

            static String
        toString(InputStream input,
            Charset encoding)

                      Get the contents of an InputStream
            as a String
            using the specified character encoding.

            static String
        toString(InputStream input,
            String encoding)

                      Get the contents of an InputStream
            as a String
            using the specified character encoding.

            static String
        toString(Reader input)

                      Get the contents of a Reader as a
            String.

            static String
        toString(URI uri)

                      Gets the contents at the given URI.

            static String
        toString(URI uri,
            Charset encoding)

                      Gets the contents at the given URI.

            static String
        toString(URI uri,
            String encoding)

                      Gets the contents at the given URI.

            static String
        toString(URL url)

                      Gets the contents at the given URL.

            static String
        toString(URL url,
            Charset encoding)

                      Gets the contents at the given URL.

            static String
        toString(URL url,
            String encoding)

                      Gets the contents at the given URL.

            static void
        write(byte[] data,
            OutputStream output)

                      Writes bytes from a byte[] to an
            OutputStream.

            static void
        write(byte[] data,
            Writer output)

                      Writes bytes from a byte[] to chars
            on a Writer
            using the default character encoding of the platform.

            static void
        write(byte[] data,
            Writer output,
            Charset encoding)

                      Writes bytes from a byte[] to chars
            on a Writer
            using the specified character encoding.

            static void
        write(byte[] data,
            Writer output,
            String encoding)

                      Writes bytes from a byte[] to chars
            on a Writer
            using the specified character encoding.

            static void
        write(char[] data,
            OutputStream output)

                      Writes chars from a char[] to bytes
            on an
            OutputStream.

            static void
        write(char[] data,
            OutputStream output,
            Charset encoding)

                      Writes chars from a char[] to bytes
            on an
            OutputStream using the specified character encoding.

            static void
        write(char[] data,
            OutputStream output,
            String encoding)

                      Writes chars from a char[] to bytes
            on an
            OutputStream using the specified character encoding.

            static void
        write(char[] data,
            Writer output)

                      Writes chars from a char[] to a
            Writer
            using the default character encoding of the platform.

            static void
        write(CharSequence data,
            OutputStream output)

                      Writes chars from a CharSequence to
            bytes on an
            OutputStream using the default character encoding of the
            platform.

            static void
        write(CharSequence data,
            OutputStream output,
            Charset encoding)

                      Writes chars from a CharSequence to
            bytes on an
            OutputStream using the specified character encoding.

            static void
        write(CharSequence data,
            OutputStream output,
            String encoding)

                      Writes chars from a CharSequence to
            bytes on an
            OutputStream using the specified character encoding.

            static void
        write(CharSequence data,
            Writer output)

                      Writes chars from a CharSequence to
            a Writer.

            static void
        write(StringBuffer data,
            OutputStream output)

                      Deprecated. replaced by
                write(CharSequence, OutputStream)

            static void
        write(StringBuffer data,
            OutputStream output,
            String encoding)

                      Deprecated. replaced by
                write(CharSequence, OutputStream, String)

            static void
        write(StringBuffer data,
            Writer output)

                      Deprecated. replaced by
                write(CharSequence, Writer)

            static void
        write(String data,
            OutputStream output)

                      Writes chars from a String to bytes
            on an
            OutputStream using the default character encoding of the
            platform.

            static void
        write(String data,
            OutputStream output,
            Charset encoding)

                      Writes chars from a String to bytes
            on an
            OutputStream using the specified character encoding.

            static void
        write(String data,
            OutputStream output,
            String encoding)

                      Writes chars from a String to bytes
            on an
            OutputStream using the specified character encoding.

            static void
        write(String data,
            Writer output)

                      Writes chars from a String to a
            Writer.

            static void
        writeLines(Collection<?> lines,
            String lineEnding,
            OutputStream output)

                      Writes the toString() value of each
            item in a collection to
            an OutputStream line by line, using the default character
            encoding of the platform and the specified line ending.

            static void
        writeLines(Collection<?> lines,
            String lineEnding,
            OutputStream output,
            Charset encoding)

                      Writes the toString() value of each
            item in a collection to
            an OutputStream line by line, using the specified character
            encoding and the specified line ending.

            static void
        writeLines(Collection<?> lines,
            String lineEnding,
            OutputStream output,
            String encoding)

                      Writes the toString() value of each
            item in a collection to
            an OutputStream line by line, using the specified character
            encoding and the specified line ending.

            static void
        writeLines(Collection<?> lines,
            String lineEnding,
            Writer writer)

                      Writes the toString() value of each
            item in a collection to
            a Writer line by line, using the specified line ending.

        Methods inherited from class java.lang.Object

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

            Field Detail

    DIR_SEPARATOR_UNIX

public static final char DIR_SEPARATOR_UNIX

The Unix directory separator character.

See Also:

Constant
                Field Values

    DIR_SEPARATOR_WINDOWS

public static final char DIR_SEPARATOR_WINDOWS

The Windows directory separator character.

See Also:

Constant
                Field Values

    DIR_SEPARATOR

public static final char DIR_SEPARATOR

The system directory separator character.

    LINE_SEPARATOR_UNIX

public static final String LINE_SEPARATOR_UNIX

The Unix line separator string.

See Also:

Constant
                Field Values

    LINE_SEPARATOR_WINDOWS

public static final String LINE_SEPARATOR_WINDOWS

The Windows line separator string.

See Also:

Constant
                Field Values

    LINE_SEPARATOR

public static final String LINE_SEPARATOR

The system line separator string.

            Constructor Detail

    IOUtils

public IOUtils()

Instances should NOT be constructed in standard programming.

            Method Detail

    close

public static void close(URLConnection conn)

Closes a URLConnection.

Parameters:

conn - the connection to close.

Since:

2.4

    closeQuietly

public static void closeQuietly(Reader input)

Unconditionally close an Reader.

            Equivalent to Reader.close(), except any exceptions will be
            ignored.
            This is typically used in finally blocks.

            Example code:

   char[] data = new char[1024];
   Reader in = null;
   try {
       in = new FileReader("foo.txt");
       in.read(data);
       in.close(); //close errors are handled
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(in);
   }

Parameters:

input - the Reader to close, may be null or already closed

    closeQuietly

public static void closeQuietly(Writer output)

Unconditionally close a Writer.

            Equivalent to Writer.close(), except any exceptions will be
            ignored.
            This is typically used in finally blocks.

            Example code:

   Writer out = null;
   try {
       out = new StringWriter();
       out.write("Hello World");
       out.close(); //close errors are handled
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(out);
   }

Parameters:

output - the Writer to close, may be null or already closed

    closeQuietly

public static void closeQuietly(InputStream input)

Unconditionally close an InputStream.

            Equivalent to InputStream.close(), except any exceptions will
            be ignored.
            This is typically used in finally blocks.

            Example code:

   byte[] data = new byte[1024];
   InputStream in = null;
   try {
       in = new FileInputStream("foo.txt");
       in.read(data);
       in.close(); //close errors are handled
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(in);
   }

Parameters:

input - the InputStream to close, may be null or already closed

    closeQuietly

public static void closeQuietly(OutputStream output)

Unconditionally close an OutputStream.

            Equivalent to OutputStream.close(), except any exceptions will
            be ignored.
            This is typically used in finally blocks.

            Example code:

 byte[] data = "Hello, World".getBytes();

 OutputStream out = null;
 try {
     out = new FileOutputStream("foo.txt");
     out.write(data);
     out.close(); //close errors are handled
 } catch (IOException e) {
     // error handling
 } finally {
     IOUtils.closeQuietly(out);
 }

Parameters:

output - the OutputStream to close, may be null or already closed

    closeQuietly

public static void closeQuietly(Closeable closeable)

Unconditionally close a Closeable.

            Equivalent to Closeable.close(), except any exceptions will be
            ignored.
            This is typically used in finally blocks.

            Example code:

   Closeable closeable = null;
   try {
       closeable = new FileReader("foo.txt");
       // process closeable
       closeable.close();
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(closeable);
   }

Parameters:

closeable - the object to close, may be null or already closed

Since:

2.0

    closeQuietly

public static void closeQuietly(Socket sock)

Unconditionally close a Socket.

            Equivalent to Socket.close(), except any exceptions will be
            ignored.
            This is typically used in finally blocks.

            Example code:

   Socket socket = null;
   try {
       socket = new Socket("http://www.foo.com/", 80);
       // process socket
       socket.close();
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(socket);
   }

Parameters:

sock - the Socket to close, may be null or already closed

Since:

2.0

    closeQuietly

public static void closeQuietly(Selector selector)

Unconditionally close a Selector.

            Equivalent to Selector.close(), except any exceptions
            will be ignored.
            This is typically used in finally blocks.

            Example code:

   Selector selector = null;
   try {
       selector = Selector.open();
       // process socket

   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(selector);
   }

Parameters:

selector - the Selector to close, may be null or already closed

Since:

2.2

    closeQuietly

public static void closeQuietly(ServerSocket sock)

Unconditionally close a ServerSocket.

            Equivalent to ServerSocket.close(), except any exceptions will
            be ignored.
            This is typically used in finally blocks.

            Example code:

   ServerSocket socket = null;
   try {
       socket = new ServerSocket();
       // process socket
       socket.close();
   } catch (Exception e) {
       // error handling
   } finally {
       IOUtils.closeQuietly(socket);
   }

Parameters:

sock - the ServerSocket to close, may be null or already closed

Since:

2.2

    toBufferedInputStream

public static InputStream toBufferedInputStream(InputStream input)
                                         throws IOException

Fetches entire contents of an InputStream and represent
        same data as result InputStream.

            This method is useful where,

Source InputStream is slow.

It has network resources associated, so we cannot keep it open for
                long time.

It has network timeout associated.

        It can be used in favor of toByteArray(InputStream),
        since it
        avoids unnecessary allocation and copy of byte[].

        This method buffers the input internally, so there is no need to use a
        BufferedInputStream.

Parameters:

input - Stream to be fully buffered.

Returns:

A fully buffered stream.

Throws:

IOException - if an I/O error occurs

Since:

2.0

    toBufferedReader

public static BufferedReader toBufferedReader(Reader reader)

Returns the given reader if it is a BufferedReader, otherwise creates a toBufferedReader
        for the given
        reader.

Parameters:

reader - the reader to wrap or return

Returns:

the given reader or a new BufferedReader for the given reader

Since:

2.2

    toByteArray

public static byte[] toByteArray(InputStream input)
                          throws IOException

Get the contents of an InputStream as a byte[].

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

    toByteArray

public static byte[] toByteArray(InputStream input,
                                 long size)
                          throws IOException

Get contents of an InputStream as a byte[].
        Use this method instead of toByteArray(InputStream)
        when InputStream size is known.
        NOTE: the method checks that the length can safely be cast to an int without truncation
        before using toByteArray(java.io.InputStream,
            int) to read into the byte array.
        (Arrays can have no more than Integer.MAX_VALUE entries anyway)

Parameters:

input - the InputStream to read from

size - the size of InputStream

Returns:

the requested byte array

Throws:

IOException - if an I/O error occurs or InputStream
                size differ from parameter size

IllegalArgumentException - if size is less than
                zero or size is greater than Integer.MAX_VALUE

Since:

2.1

See Also:

toByteArray(java.io.InputStream,
                int)

    toByteArray

public static byte[] toByteArray(InputStream input,
                                 int size)
                          throws IOException

Get the contents of an InputStream as a byte[].
        Use this method instead of toByteArray(InputStream)
        when InputStream size is known

Parameters:

input - the InputStream to read from

size - the size of InputStream

Returns:

the requested byte array

Throws:

IOException - if an I/O error occurs or InputStream
                size differ from parameter size

IllegalArgumentException - if size is less than
                zero

Since:

2.1

    toByteArray

public static byte[] toByteArray(Reader input)
                          throws IOException

Get the contents of a Reader as a byte[]
        using the default character encoding of the platform.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

    toByteArray

public static byte[] toByteArray(Reader input,
                                 Charset encoding)
                          throws IOException

Get the contents of a Reader as a byte[]
        using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

encoding - the encoding to use, null means platform default

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

2.3

    toByteArray

public static byte[] toByteArray(Reader input,
                                 String encoding)
                          throws IOException

Get the contents of a Reader as a byte[]
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

encoding - the encoding to use, null means platform default

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    toByteArray

@Deprecated
public static byte[] toByteArray(String input)
                          throws IOException

Deprecated. Use String.getBytes()

Get the contents of a String as a byte[]
                using the default character encoding of the platform.

            This is the same as String.getBytes().

Parameters:

input - the String to convert

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs (never
                occurs)

    toByteArray

public static byte[] toByteArray(URI uri)
                          throws IOException

Get the contents of a URI as a byte[].

Parameters:

uri - the URI to read

Returns:

the requested byte array

Throws:

NullPointerException - if the uri is null

IOException - if an I/O exception occurs

Since:

2.4

    toByteArray

public static byte[] toByteArray(URL url)
                          throws IOException

Get the contents of a URL as a byte[].

Parameters:

url - the URL to read

Returns:

the requested byte array

Throws:

NullPointerException - if the input is null

IOException - if an I/O exception occurs

Since:

2.4

    toByteArray

public static byte[] toByteArray(URLConnection urlConn)
                          throws IOException

Get the contents of a URLConnection as a byte[].

Parameters:

urlConn - the URLConnection to read

Returns:

the requested byte array

Throws:

NullPointerException - if the urlConn is null

IOException - if an I/O exception occurs

Since:

2.4

    toCharArray

public static char[] toCharArray(InputStream is)
                          throws IOException

Get the contents of an InputStream as a character array
        using the default character encoding of the platform.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

is - the InputStream to read from

Returns:

the requested character array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

1.1

    toCharArray

public static char[] toCharArray(InputStream is,
                                 Charset encoding)
                          throws IOException

Get the contents of an InputStream as a character array
        using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

is - the InputStream to read from

encoding - the encoding to use, null means platform default

Returns:

the requested character array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

2.3

    toCharArray

public static char[] toCharArray(InputStream is,
                                 String encoding)
                          throws IOException

Get the contents of an InputStream as a character array
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

is - the InputStream to read from

encoding - the encoding to use, null means platform default

Returns:

the requested character array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    toCharArray

public static char[] toCharArray(Reader input)
                          throws IOException

Get the contents of a Reader as a character array.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

Returns:

the requested character array

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

1.1

    toString

public static String toString(InputStream input)
                       throws IOException

Get the contents of an InputStream as a String
        using the default character encoding of the platform.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

    toString

public static String toString(InputStream input,
                              Charset encoding)
                       throws IOException

Get the contents of an InputStream as a String
        using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

encoding - the encoding to use, null means platform default

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

2.3

    toString

public static String toString(InputStream input,
                              String encoding)
                       throws IOException

Get the contents of an InputStream as a String
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

encoding - the encoding to use, null means platform default

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

    toString

public static String toString(Reader input)
                       throws IOException

Get the contents of a Reader as a String.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

    toString

public static String toString(URI uri)
                       throws IOException

Gets the contents at the given URI.

Parameters:

uri - The URI source.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

Since:

2.1

    toString

public static String toString(URI uri,
                              Charset encoding)
                       throws IOException

Gets the contents at the given URI.

Parameters:

uri - The URI source.

encoding - The encoding name for the URL contents.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

Since:

2.3.

    toString

public static String toString(URI uri,
                              String encoding)
                       throws IOException

Gets the contents at the given URI.

Parameters:

uri - The URI source.

encoding - The encoding name for the URL contents.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

2.1

    toString

public static String toString(URL url)
                       throws IOException

Gets the contents at the given URL.

Parameters:

url - The URL source.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

Since:

2.1

    toString

public static String toString(URL url,
                              Charset encoding)
                       throws IOException

Gets the contents at the given URL.

Parameters:

url - The URL source.

encoding - The encoding name for the URL contents.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

Since:

2.3

    toString

public static String toString(URL url,
                              String encoding)
                       throws IOException

Gets the contents at the given URL.

Parameters:

url - The URL source.

encoding - The encoding name for the URL contents.

Returns:

The contents of the URL as a String.

Throws:

IOException - if an I/O exception occurs.

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

2.1

    toString

@Deprecated
public static String toString(byte[] input)
                       throws IOException

Deprecated. Use String.String(byte[])

Get the contents of a byte[] as a String
        using the default character encoding of the platform.

Parameters:

input - the byte array to read from

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs (never
                occurs)

    toString

public static String toString(byte[] input,
                              String encoding)
                       throws IOException

Get the contents of a byte[] as a String
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

Parameters:

input - the byte array to read from

encoding - the encoding to use, null means platform default

Returns:

the requested String

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs (never
                occurs)

    readLines

public static List<String> readLines(InputStream input)
                              throws IOException

Get the contents of an InputStream as a list of Strings,
        one entry per line, using the default character encoding of the platform.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from, not null

Returns:

the list of Strings, never null

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

1.1

    readLines

public static List<String> readLines(InputStream input,
                                     Charset encoding)
                              throws IOException

Get the contents of an InputStream as a list of Strings,
        one entry per line, using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from, not null

encoding - the encoding to use, null means platform default

Returns:

the list of Strings, never null

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

2.3

    readLines

public static List<String> readLines(InputStream input,
                                     String encoding)
                              throws IOException

Get the contents of an InputStream as a list of Strings,
        one entry per line, using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from, not null

encoding - the encoding to use, null means platform default

Returns:

the list of Strings, never null

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    readLines

public static List<String> readLines(Reader input)
                              throws IOException

Get the contents of a Reader as a list of Strings,
        one entry per line.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from, not null

Returns:

the list of Strings, never null

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

1.1

    lineIterator

public static LineIterator lineIterator(Reader reader)

Return an Iterator for the lines in a Reader.

            LineIterator holds a reference to the open
            Reader specified here. When you have finished with the
            iterator you should close the reader to free internal resources.
            This can be done by closing the reader directly, or by calling
            LineIterator.close()
            or LineIterator.closeQuietly(LineIterator).

            The recommended usage pattern is:

 try {
   LineIterator it = IOUtils.lineIterator(reader);
   while (it.hasNext()) {
     String line = it.nextLine();
     /// do something with line
   }
 } finally {
   IOUtils.closeQuietly(reader);
 }

Parameters:

reader - the Reader to read from, not null

Returns:

an Iterator of the lines in the reader, never null

Throws:

IllegalArgumentException - if the reader is null

Since:

1.2

    lineIterator

public static LineIterator lineIterator(InputStream input,
                                        Charset encoding)
                                 throws IOException

Return an Iterator for the lines in an InputStream, using
        the character encoding specified (or default encoding if null).

            LineIterator holds a reference to the open
            InputStream specified here. When you have finished with
            the iterator you should close the stream to free internal resources.
            This can be done by closing the stream directly, or by calling
            LineIterator.close()
            or LineIterator.closeQuietly(LineIterator).

            The recommended usage pattern is:

 try {
   LineIterator it = IOUtils.lineIterator(stream, charset);
   while (it.hasNext()) {
     String line = it.nextLine();
     /// do something with line
   }
 } finally {
   IOUtils.closeQuietly(stream);
 }

Parameters:

input - the InputStream to read from, not null

encoding - the encoding to use, null means platform default

Returns:

an Iterator of the lines in the reader, never null

Throws:

IllegalArgumentException - if the input is null

IOException - if an I/O error occurs, such as
                if the encoding is invalid

Since:

2.3

    lineIterator

public static LineIterator lineIterator(InputStream input,
                                        String encoding)
                                 throws IOException

Return an Iterator for the lines in an InputStream, using
        the character encoding specified (or default encoding if null).

            LineIterator holds a reference to the open
            InputStream specified here. When you have finished with
            the iterator you should close the stream to free internal resources.
            This can be done by closing the stream directly, or by calling
            LineIterator.close()
            or LineIterator.closeQuietly(LineIterator).

            The recommended usage pattern is:

 try {
   LineIterator it = IOUtils.lineIterator(stream, "UTF-8");
   while (it.hasNext()) {
     String line = it.nextLine();
     /// do something with line
   }
 } finally {
   IOUtils.closeQuietly(stream);
 }

Parameters:

input - the InputStream to read from, not null

encoding - the encoding to use, null means platform default

Returns:

an Iterator of the lines in the reader, never null

Throws:

IllegalArgumentException - if the input is null

IOException - if an I/O error occurs, such as
                if the encoding is invalid

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.2

    toInputStream

public static InputStream toInputStream(CharSequence input)

Convert the specified CharSequence to an input stream, encoded as bytes
        using the default character encoding of the platform.

Parameters:

input - the CharSequence to convert

Returns:

an input stream

Since:

2.0

    toInputStream

public static InputStream toInputStream(CharSequence input,
                                        Charset encoding)

Convert the specified CharSequence to an input stream, encoded as bytes
        using the specified character encoding.

Parameters:

input - the CharSequence to convert

encoding - the encoding to use, null means platform default

Returns:

an input stream

Since:

2.3

    toInputStream

public static InputStream toInputStream(CharSequence input,
                                        String encoding)
                                 throws IOException

Convert the specified CharSequence to an input stream, encoded as bytes
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

Parameters:

input - the CharSequence to convert

encoding - the encoding to use, null means platform default

Returns:

an input stream

Throws:

IOException - if the encoding is invalid

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

2.0

    toInputStream

public static InputStream toInputStream(String input)

Convert the specified string to an input stream, encoded as bytes
        using the default character encoding of the platform.

Parameters:

input - the string to convert

Returns:

an input stream

Since:

1.1

    toInputStream

public static InputStream toInputStream(String input,
                                        Charset encoding)

Convert the specified string to an input stream, encoded as bytes
        using the specified character encoding.

Parameters:

input - the string to convert

encoding - the encoding to use, null means platform default

Returns:

an input stream

Since:

2.3

    toInputStream

public static InputStream toInputStream(String input,
                                        String encoding)
                                 throws IOException

Convert the specified string to an input stream, encoded as bytes
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

Parameters:

input - the string to convert

encoding - the encoding to use, null means platform default

Returns:

an input stream

Throws:

IOException - if the encoding is invalid

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    write

public static void write(byte[] data,
                         OutputStream output)
                  throws IOException

Writes bytes from a byte[] to an OutputStream.

Parameters:

data - the byte array to write, do not modify during output,
                null ignored

output - the OutputStream to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(byte[] data,
                         Writer output)
                  throws IOException

Writes bytes from a byte[] to chars on a Writer
        using the default character encoding of the platform.

            This method uses String.String(byte[]).

Parameters:

data - the byte array to write, do not modify during output,
                null ignored

output - the Writer to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(byte[] data,
                         Writer output,
                         Charset encoding)
                  throws IOException

Writes bytes from a byte[] to chars on a Writer
        using the specified character encoding.

            This method uses String.String(byte[], String).

Parameters:

data - the byte array to write, do not modify during output,
                null ignored

output - the Writer to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.3

    write

public static void write(byte[] data,
                         Writer output,
                         String encoding)
                  throws IOException

Writes bytes from a byte[] to chars on a Writer
        using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method uses String.String(byte[], String).

Parameters:

data - the byte array to write, do not modify during output,
                null ignored

output - the Writer to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    write

public static void write(char[] data,
                         Writer output)
                  throws IOException

Writes chars from a char[] to a Writer
        using the default character encoding of the platform.

Parameters:

data - the char array to write, do not modify during output,
                null ignored

output - the Writer to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(char[] data,
                         OutputStream output)
                  throws IOException

Writes chars from a char[] to bytes on an
        OutputStream.

            This method uses String.String(char[]) and
            String.getBytes().

Parameters:

data - the char array to write, do not modify during output,
                null ignored

output - the OutputStream to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(char[] data,
                         OutputStream output,
                         Charset encoding)
                  throws IOException

Writes chars from a char[] to bytes on an
        OutputStream using the specified character encoding.

            This method uses String.String(char[]) and
            String.getBytes(String).

Parameters:

data - the char array to write, do not modify during output,
                null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.3

    write

public static void write(char[] data,
                         OutputStream output,
                         String encoding)
                  throws IOException

Writes chars from a char[] to bytes on an
        OutputStream using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method uses String.String(char[]) and
            String.getBytes(String).

Parameters:

data - the char array to write, do not modify during output,
                null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    write

public static void write(CharSequence data,
                         Writer output)
                  throws IOException

Writes chars from a CharSequence to a Writer.

Parameters:

data - the CharSequence to write, null ignored

output - the Writer to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.0

    write

public static void write(CharSequence data,
                         OutputStream output)
                  throws IOException

Writes chars from a CharSequence to bytes on an
        OutputStream using the default character encoding of the
        platform.

            This method uses String.getBytes().

Parameters:

data - the CharSequence to write, null ignored

output - the OutputStream to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.0

    write

public static void write(CharSequence data,
                         OutputStream output,
                         Charset encoding)
                  throws IOException

Writes chars from a CharSequence to bytes on an
        OutputStream using the specified character encoding.

            This method uses String.getBytes(String).

Parameters:

data - the CharSequence to write, null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.3

    write

public static void write(CharSequence data,
                         OutputStream output,
                         String encoding)
                  throws IOException

Writes chars from a CharSequence to bytes on an
        OutputStream using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method uses String.getBytes(String).

Parameters:

data - the CharSequence to write, null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

2.0

    write

public static void write(String data,
                         Writer output)
                  throws IOException

Writes chars from a String to a Writer.

Parameters:

data - the String to write, null ignored

output - the Writer to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(String data,
                         OutputStream output)
                  throws IOException

Writes chars from a String to bytes on an
        OutputStream using the default character encoding of the
        platform.

            This method uses String.getBytes().

Parameters:

data - the String to write, null ignored

output - the OutputStream to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

public static void write(String data,
                         OutputStream output,
                         Charset encoding)
                  throws IOException

Writes chars from a String to bytes on an
        OutputStream using the specified character encoding.

            This method uses String.getBytes(String).

Parameters:

data - the String to write, null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

2.3

    write

public static void write(String data,
                         OutputStream output,
                         String encoding)
                  throws IOException

Writes chars from a String to bytes on an
        OutputStream using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method uses String.getBytes(String).

Parameters:

data - the String to write, null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    write

@Deprecated
public static void write(StringBuffer data,
                                    Writer output)
                  throws IOException

Deprecated. replaced by write(CharSequence, Writer)

Writes chars from a StringBuffer to a Writer.

Parameters:

data - the StringBuffer to write, null ignored

output - the Writer to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

@Deprecated
public static void write(StringBuffer data,
                                    OutputStream output)
                  throws IOException

Deprecated. replaced by write(CharSequence, OutputStream)

Writes chars from a StringBuffer to bytes on an
                OutputStream using the default character encoding of the
                platform.

            This method uses String.getBytes().

Parameters:

data - the StringBuffer to write, null ignored

output - the OutputStream to write to

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

Since:

1.1

    write

@Deprecated
public static void write(StringBuffer data,
                                    OutputStream output,
                                    String encoding)
                  throws IOException

Deprecated. replaced by write(CharSequence, OutputStream, String)

Writes chars from a StringBuffer to bytes on an
                OutputStream using the specified character encoding.

            Character encoding names can be found at
            IANA.

            This method uses String.getBytes(String).

Parameters:

data - the StringBuffer to write, null ignored

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    writeLines

public static void writeLines(Collection<?> lines,
                              String lineEnding,
                              OutputStream output)
                       throws IOException

Writes the toString() value of each item in a collection to
        an OutputStream line by line, using the default character
        encoding of the platform and the specified line ending.

Parameters:

lines - the lines to write, null entries produce blank lines

lineEnding - the line separator to use, null is system default

output - the OutputStream to write to, not null, not closed

Throws:

NullPointerException - if the output is null

IOException - if an I/O error occurs

Since:

1.1

    writeLines

public static void writeLines(Collection<?> lines,
                              String lineEnding,
                              OutputStream output,
                              Charset encoding)
                       throws IOException

Writes the toString() value of each item in a collection to
        an OutputStream line by line, using the specified character
        encoding and the specified line ending.

Parameters:

lines - the lines to write, null entries produce blank lines

lineEnding - the line separator to use, null is system default

output - the OutputStream to write to, not null, not closed

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the output is null

IOException - if an I/O error occurs

Since:

2.3

    writeLines

public static void writeLines(Collection<?> lines,
                              String lineEnding,
                              OutputStream output,
                              String encoding)
                       throws IOException

Writes the toString() value of each item in a collection to
        an OutputStream line by line, using the specified character
        encoding and the specified line ending.

            Character encoding names can be found at
            IANA.

Parameters:

lines - the lines to write, null entries produce blank lines

lineEnding - the line separator to use, null is system default

output - the OutputStream to write to, not null, not closed

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the output is null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    writeLines

public static void writeLines(Collection<?> lines,
                              String lineEnding,
                              Writer writer)
                       throws IOException

Writes the toString() value of each item in a collection to
        a Writer line by line, using the specified line ending.

Parameters:

lines - the lines to write, null entries produce blank lines

lineEnding - the line separator to use, null is system default

writer - the Writer to write to, not null, not closed

Throws:

NullPointerException - if the input is null

IOException - if an I/O error occurs

Since:

1.1

    copy

public static int copy(InputStream input,
                       OutputStream output)
                throws IOException

Copy bytes from an InputStream to an
        OutputStream.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            Large streams (over 2GB) will return a bytes copied value of
            -1 after the copy has completed since the correct
            number of bytes cannot be returned as an int. For large streams
            use the copyLarge(InputStream, OutputStream) method.

Parameters:

input - the InputStream to read from

output - the OutputStream to write to

Returns:

the number of bytes copied, or -1 if > Integer.MAX_VALUE

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.1

    copyLarge

public static long copyLarge(InputStream input,
                             OutputStream output)
                      throws IOException

Copy bytes from a large (over 2GB) InputStream to an
        OutputStream.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            The buffer size is given by DEFAULT_BUFFER_SIZE.

Parameters:

input - the InputStream to read from

output - the OutputStream to write to

Returns:

the number of bytes copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.3

    copyLarge

public static long copyLarge(InputStream input,
                             OutputStream output,
                             byte[] buffer)
                      throws IOException

Copy bytes from a large (over 2GB) InputStream to an
        OutputStream.

            This method uses the provided buffer, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

output - the OutputStream to write to

buffer - the buffer to use for the copy

Returns:

the number of bytes copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copyLarge

public static long copyLarge(InputStream input,
                             OutputStream output,
                             long inputOffset,
                             long length)
                      throws IOException

Copy some or all bytes from a large (over 2GB) InputStream to an
        OutputStream, optionally skipping input bytes.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            The buffer size is given by DEFAULT_BUFFER_SIZE.

Parameters:

input - the InputStream to read from

output - the OutputStream to write to

inputOffset - : number of bytes to skip from input before copying
                -ve values are ignored

length - : number of bytes to copy. -ve means all

Returns:

the number of bytes copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copyLarge

public static long copyLarge(InputStream input,
                             OutputStream output,
                             long inputOffset,
                             long length,
                             byte[] buffer)
                      throws IOException

Copy some or all bytes from a large (over 2GB) InputStream to an
        OutputStream, optionally skipping input bytes.

            This method uses the provided buffer, so there is no need to use a
            BufferedInputStream.

Parameters:

input - the InputStream to read from

output - the OutputStream to write to

inputOffset - : number of bytes to skip from input before copying
                -ve values are ignored

length - : number of bytes to copy. -ve means all

buffer - the buffer to use for the copy

Returns:

the number of bytes copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copy

public static void copy(InputStream input,
                        Writer output)
                 throws IOException

Copy bytes from an InputStream to chars on a
        Writer using the default character encoding of the platform.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            This method uses InputStreamReader.

Parameters:

input - the InputStream to read from

output - the Writer to write to

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.1

    copy

public static void copy(InputStream input,
                        Writer output,
                        Charset encoding)
                 throws IOException

Copy bytes from an InputStream to chars on a
        Writer using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            This method uses InputStreamReader.

Parameters:

input - the InputStream to read from

output - the Writer to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.3

    copy

public static void copy(InputStream input,
                        Writer output,
                        String encoding)
                 throws IOException

Copy bytes from an InputStream to chars on a
        Writer using the specified character encoding.

            This method buffers the input internally, so there is no need to use a
            BufferedInputStream.

            Character encoding names can be found at
            IANA.

            This method uses InputStreamReader.

Parameters:

input - the InputStream to read from

output - the Writer to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    copy

public static int copy(Reader input,
                       Writer output)
                throws IOException

Copy chars from a Reader to a Writer.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            Large streams (over 2GB) will return a chars copied value of
            -1 after the copy has completed since the correct
            number of chars cannot be returned as an int. For large streams
            use the copyLarge(Reader, Writer) method.

Parameters:

input - the Reader to read from

output - the Writer to write to

Returns:

the number of characters copied, or -1 if > Integer.MAX_VALUE

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.1

    copyLarge

public static long copyLarge(Reader input,
                             Writer output)
                      throws IOException

Copy chars from a large (over 2GB) Reader to a Writer.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            The buffer size is given by DEFAULT_BUFFER_SIZE.

Parameters:

input - the Reader to read from

output - the Writer to write to

Returns:

the number of characters copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.3

    copyLarge

public static long copyLarge(Reader input,
                             Writer output,
                             char[] buffer)
                      throws IOException

Copy chars from a large (over 2GB) Reader to a Writer.

            This method uses the provided buffer, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

output - the Writer to write to

buffer - the buffer to be used for the copy

Returns:

the number of characters copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copyLarge

public static long copyLarge(Reader input,
                             Writer output,
                             long inputOffset,
                             long length)
                      throws IOException

Copy some or all chars from a large (over 2GB) InputStream to an
        OutputStream, optionally skipping input chars.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            The buffer size is given by DEFAULT_BUFFER_SIZE.

Parameters:

input - the Reader to read from

output - the Writer to write to

inputOffset - : number of chars to skip from input before copying
                -ve values are ignored

length - : number of chars to copy. -ve means all

Returns:

the number of chars copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copyLarge

public static long copyLarge(Reader input,
                             Writer output,
                             long inputOffset,
                             long length,
                             char[] buffer)
                      throws IOException

Copy some or all chars from a large (over 2GB) InputStream to an
        OutputStream, optionally skipping input chars.

            This method uses the provided buffer, so there is no need to use a
            BufferedReader.

Parameters:

input - the Reader to read from

output - the Writer to write to

inputOffset - : number of chars to skip from input before copying
                -ve values are ignored

length - : number of chars to copy. -ve means all

buffer - the buffer to be used for the copy

Returns:

the number of chars copied

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.2

    copy

public static void copy(Reader input,
                        OutputStream output)
                 throws IOException

Copy chars from a Reader to bytes on an
        OutputStream using the default character encoding of the
        platform, and calling flush.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            Due to the implementation of OutputStreamWriter, this method performs a
            flush.

            This method uses OutputStreamWriter.

Parameters:

input - the Reader to read from

output - the OutputStream to write to

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

1.1

    copy

public static void copy(Reader input,
                        OutputStream output,
                        Charset encoding)
                 throws IOException

Copy chars from a Reader to bytes on an
        OutputStream using the specified character encoding, and
        calling flush.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            Due to the implementation of OutputStreamWriter, this method performs a
            flush.

            This method uses OutputStreamWriter.

Parameters:

input - the Reader to read from

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

Since:

2.3

    copy

public static void copy(Reader input,
                        OutputStream output,
                        String encoding)
                 throws IOException

Copy chars from a Reader to bytes on an
        OutputStream using the specified character encoding, and
        calling flush.

            This method buffers the input internally, so there is no need to use a
            BufferedReader.

            Character encoding names can be found at
            IANA.

            Due to the implementation of OutputStreamWriter, this method performs a
            flush.

            This method uses OutputStreamWriter.

Parameters:

input - the Reader to read from

output - the OutputStream to write to

encoding - the encoding to use, null means platform default

Throws:

NullPointerException - if the input or output is
                null

IOException - if an I/O error occurs

UnsupportedCharsetException - thrown
                instead of UnsupportedEncodingException in version
                2.2 if the encoding is not
                supported.

Since:

1.1

    contentEquals

public static boolean contentEquals(InputStream input1,
                                    InputStream input2)
                             throws IOException

Compare the contents of two Streams to determine if they are equal or
        not.

            This method buffers the input internally using
            BufferedInputStream if they are not already buffered.

Parameters:

input1 - the first stream

input2 - the second stream

Returns:

true if the content of the streams are equal or they both don't
                exist, false otherwise

Throws:

NullPointerException - if either input is null

IOException - if an I/O error occurs

    contentEquals

public static boolean contentEquals(Reader input1,
                                    Reader input2)
                             throws IOException

Compare the contents of two Readers to determine if they are equal or
        not.

            This method buffers the input internally using
            BufferedReader if they are not already buffered.

Parameters:

input1 - the first reader

input2 - the second reader

Returns:

true if the content of the readers are equal or they both don't
                exist, false otherwise

Throws:

NullPointerException - if either input is null

IOException - if an I/O error occurs

Since:

1.1

    contentEqualsIgnoreEOL

public static boolean contentEqualsIgnoreEOL(Reader input1,
                                             Reader input2)
                                      throws IOException

Compare the contents of two Readers to determine if they are equal or
        not, ignoring EOL characters.

            This method buffers the input internally using
            BufferedReader if they are not already buffered.

Parameters:

input1 - the first reader

input2 - the second reader

Returns:

true if the content of the readers are equal (ignoring EOL differences), false otherwise

Throws:

NullPointerException - if either input is null

IOException - if an I/O error occurs

Since:

2.2

    skip

public static long skip(InputStream input,
                        long toSkip)
                 throws IOException

Skip bytes from an input byte stream.
        This implementation guarantees that it will read as many bytes
        as possible before giving up; this may not always be the case for
        subclasses of Reader.

Parameters:

input - byte stream to skip

toSkip - number of bytes to skip.

Returns:

number of bytes actually skipped.

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if toSkip is negative

Since:

2.0

See Also:

                InputStream.skip(long)

    skip

public static long skip(Reader input,
                        long toSkip)
                 throws IOException

Skip characters from an input character stream.
        This implementation guarantees that it will read as many characters
        as possible before giving up; this may not always be the case for
        subclasses of Reader.

Parameters:

input - character stream to skip

toSkip - number of characters to skip.

Returns:

number of characters actually skipped.

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if toSkip is negative

Since:

2.0

See Also:

Reader.skip(long)

    skipFully

public static void skipFully(InputStream input,
                             long toSkip)
                      throws IOException

Skip the requested number of bytes or fail if there are not enough left.

            This allows for the possibility that InputStream.skip(long) may
            not skip as many bytes as requested (most likely because of reaching EOF).

Parameters:

input - stream to skip

toSkip - the number of bytes to skip

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if toSkip is negative

EOFException - if the number of bytes skipped
                was incorrect

Since:

2.0

See Also:

                InputStream.skip(long)

    skipFully

public static void skipFully(Reader input,
                             long toSkip)
                      throws IOException

Skip the requested number of characters or fail if there are not enough left.

            This allows for the possibility that Reader.skip(long) may
            not skip as many characters as requested (most likely because of reaching EOF).

Parameters:

input - stream to skip

toSkip - the number of characters to skip

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if toSkip is negative

EOFException - if the number of characters
                skipped was incorrect

Since:

2.0

See Also:

Reader.skip(long)

    read

public static int read(Reader input,
                       char[] buffer,
                       int offset,
                       int length)
                throws IOException

Read characters from an input character stream.
        This implementation guarantees that it will read as many characters
        as possible before giving up; this may not always be the case for
        subclasses of Reader.

Parameters:

input - where to read input from

buffer - destination

offset - inital offset into buffer

length - length to read, must be >= 0

Returns:

actual length read; may be less than requested if EOF was reached

Throws:

IOException - if a read error occurs

Since:

2.2

    read

public static int read(Reader input,
                       char[] buffer)
                throws IOException

Read characters from an input character stream.
        This implementation guarantees that it will read as many characters
        as possible before giving up; this may not always be the case for
        subclasses of Reader.

Parameters:

input - where to read input from

buffer - destination

Returns:

actual length read; may be less than requested if EOF was reached

Throws:

IOException - if a read error occurs

Since:

2.2

    read

public static int read(InputStream input,
                       byte[] buffer,
                       int offset,
                       int length)
                throws IOException

Read bytes from an input stream.
        This implementation guarantees that it will read as many bytes
        as possible before giving up; this may not always be the case for
        subclasses of InputStream.

Parameters:

input - where to read input from

buffer - destination

offset - inital offset into buffer

length - length to read, must be >= 0

Returns:

actual length read; may be less than requested if EOF was reached

Throws:

IOException - if a read error occurs

Since:

2.2

    read

public static int read(InputStream input,
                       byte[] buffer)
                throws IOException

Read bytes from an input stream.
        This implementation guarantees that it will read as many bytes
        as possible before giving up; this may not always be the case for
        subclasses of InputStream.

Parameters:

input - where to read input from

buffer - destination

Returns:

actual length read; may be less than requested if EOF was reached

Throws:

IOException - if a read error occurs

Since:

2.2

    readFully

public static void readFully(Reader input,
                             char[] buffer,
                             int offset,
                             int length)
                      throws IOException

Read the requested number of characters or fail if there are not enough left.

            This allows for the possibility that Reader.read(char[], int, int) may
            not read as many characters as requested (most likely because of reaching EOF).

Parameters:

input - where to read input from

buffer - destination

offset - inital offset into buffer

length - length to read, must be >= 0

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if length is negative

EOFException - if the number of characters
                read was incorrect

Since:

2.2

    readFully

public static void readFully(Reader input,
                             char[] buffer)
                      throws IOException

Read the requested number of characters or fail if there are not enough left.

            This allows for the possibility that Reader.read(char[], int, int) may
            not read as many characters as requested (most likely because of reaching EOF).

Parameters:

input - where to read input from

buffer - destination

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if length is negative

EOFException - if the number of characters
                read was incorrect

Since:

2.2

    readFully

public static void readFully(InputStream input,
                             byte[] buffer,
                             int offset,
                             int length)
                      throws IOException

Read the requested number of bytes or fail if there are not enough left.

            This allows for the possibility that InputStream.read(byte[], int, int) may
            not read as many bytes as requested (most likely because of reaching EOF).

Parameters:

input - where to read input from

buffer - destination

offset - inital offset into buffer

length - length to read, must be >= 0

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if length is negative

EOFException - if the number of bytes read was
                incorrect

Since:

2.2

    readFully

public static void readFully(InputStream input,
                             byte[] buffer)
                      throws IOException

Read the requested number of bytes or fail if there are not enough left.

            This allows for the possibility that InputStream.read(byte[], int, int) may
            not read as many bytes as requested (most likely because of reaching EOF).

Parameters:

input - where to read input from

buffer - destination

Throws:

IOException - if there is a problem reading
                the file

IllegalArgumentException - if length is negative

EOFException - if the number of bytes read was
                incorrect

Since:

2.2

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text:
use strict;
use warnings;
use File::Basename;
use BitQC;

######################################################################################
# INITIALISE BITQC MODULE
######################################################################################

# Make BitQC object
# settings will come from environment variables
my $BitQC = new BitQC();

# Load bitqc configuration from the given database
$BitQC->load(
	'script_args' => {
		'bam'			=> { type => 'string' }
	}
);

######################################################################################
# COMMANDS AND VARIABLES
######################################################################################

my $BAM 	= $BitQC->getRunConfig('bam');
my $REMOVE  = $BitQC->getRunConfig('remove');
my $BUILD   = $BitQC->getRunConfig('genomebuild');

#Get command
my $GATK_COMMAND = $BitQC->getCommand('gatk');
my $ANALYSECOVARIATE_COMMAND = $BitQC->getCommand('analysecovariate');

#Get necessary executables and paths
my $BITQC_NODE_STORAGE = $BitQC->{node_config}->{paths}->{nodetempdir}->{dir};

#Get index for given organismbuild
my $GATK_INDEX = $BitQC->getGenomeIndex('gatk');

#SNP database
my $SNP_VCF =
    $BitQC->{node_config}->{paths}->{genomedir}->{dir}
  . $BUILD . "/"
  . $BitQC->{genome}->{files}->{dbsnp}->{path};

######################################################################################
# START GATK RECALIBRATION OF FASTQ FILE
######################################################################################

my $bamname;
my $bampath;
( $bamname, $bampath, my $bamext ) = fileparse( $BAM, '\..*' );

# set some file names
my $infile         = $bampath . $bamname . "-norecal.bam";
my $pre_recalfile  = $bampath . $bamname . "-pre-recal-calmetrics.csv";
my $pre_recalfolder = $bampath . "covariate_plots_pre/";
mkdir $pre_recalfolder;
my $post_recalfile = $bampath . $bamname . "-post-recal-calmetrics.csv";
my $post_recalfolder = $bampath . "covariate_plots_post/";
mkdir $post_recalfolder;

# rename the input file (and its index)
rename( $BAM, $infile );
rename( $bampath . $bamname . ".bai", $bampath . $bamname . "-norecal.bai" );

$BitQC->log_message( message =>
	  "Performing base quality recalibration for $BAM" );

$BitQC->run_and_log(
	message => "Counting covariates",
	command =>
"$GATK_COMMAND -l INFO "
	  . "-R $GATK_INDEX --knownSites $SNP_VCF -I $infile "
	  . "-T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate "
	  . "-cov CycleCovariate -cov DinucCovariate -recalFile $pre_recalfile"
);

$BitQC->run_and_log(
	message => "Recalibrating quality scores",
	command =>
"$GATK_COMMAND -l INFO -R $GATK_INDEX -I $infile -T TableRecalibration --out $BAM -recalFile $pre_recalfile"
);

$BitQC->run_and_log(
	message => "Generating plots and reports.",
	command =>
"$ANALYSECOVARIATE_COMMAND --recal_file $pre_recalfile --output_dir $pre_recalfolder"
);

$BitQC->run_and_log(
	message => "Recounting covariates after recalibration",
	command =>
"$GATK_COMMAND -l INFO -R $GATK_INDEX --knownSites $SNP_VCF -I $BAM -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile $post_recalfile"
);

$BitQC->run_and_log(
	message => "Generating plots and reports.",
	command =>
"$ANALYSECOVARIATE_COMMAND --recal_file $post_recalfile --output_dir $post_recalfolder"
);

$BitQC->log_message( message =>
	  "Moving file from local to shared directory" );

######################################################################################
# FINISH SCRIPT
######################################################################################

if ($REMOVE) {
	unlink($infile);
	unlink( $bampath . $bamname . "-norecal.bai" );
	$BitQC->log_message( message => "Removed input $infile file" );
}

# finish logging
$BitQC->finish_log(
	message => "Job completed: $BAM file recalibrated using the GATK" );

redpajama_set_name: RedPajamaGithub