org.biojava.nbio.core.sequence.io

Class BufferedReaderBytesRead

java.lang.Object

java.io.Reader

org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

All Implemented Interfaces:

Closeable, AutoCloseable, Readable

public class BufferedReaderBytesRead
extends Reader

Need to keep track of actual bytes read and take advantage of buffered reader performance. Took java source for BufferedReader and added BytesRead functionality
---------- original buffered reader ----------------------
Reads text from a character-input stream, buffering characters so as to provide for the efficient reading of characters, arrays, and lines.

The buffer size may be specified, or the default size may be used. The default is large enough for most purposes.

In general, each read request made of a Reader causes a corresponding read request to be made of the underlying character or byte stream. It is therefore advisable to wrap a BufferedReaderBytesRead around any Reader whose read() operations may be costly, such as FileReaders and InputStreamReaders. For example,

 BufferedReaderBytesRead in
   = new BufferedReaderBytesRead(new FileReader("foo.in"));
 

will buffer the input from the specified file. Without buffering, each invocation of read() or readLine() could cause bytes to be read from the file, converted into characters, and then returned, which can be very inefficient.

Programs that use DataInputStreams for textual input can be localized by replacing each DataInputStream with an appropriate BufferedReaderBytesRead.

Since:

JDK1.1

Version:

1.37, 06/03/15

Author:

Mark Reinhold, Scooter Willis <willishf at gmail dot com>

See Also:

FileReader, InputStreamReader

Field Summary

Fields inherited from class java.io.Reader

lock

Constructor Summary

Constructors

Constructor and Description
BufferedReaderBytesRead(Reader in) Creates a buffering character-input stream that uses a default-sized input buffer.
BufferedReaderBytesRead(Reader in, int sz) Creates a buffering character-input stream that uses an input buffer of the specified size.

Method Summary

Modifier and Type	Method and Description
void	close()
long	getBytesRead() Keep track of bytesread via ReadLine to account for CR-LF in the stream.
void	mark(int readAheadLimit) Marks the present position in the stream.
boolean	markSupported() Tells whether this stream supports the mark() operation, which it does.
int	read() Reads a single character.
int	read(char[] cbuf, int off, int len) Reads characters into a portion of an array.
String	readLine() Reads a line of text.
boolean	ready() Tells whether this stream is ready to be read.
void	reset() Resets the stream to the most recent mark.
long	skip(long n) Skips characters.

Methods inherited from class java.io.Reader

read, read

Methods inherited from class java.lang.Object

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

Constructor Detail

BufferedReaderBytesRead

public BufferedReaderBytesRead(Reader in,
                               int sz)

Creates a buffering character-input stream that uses an input buffer of the specified size.

Parameters:

in - A Reader

sz - Input-buffer size

Throws:

IllegalArgumentException - If sz is <= 0

BufferedReaderBytesRead

public BufferedReaderBytesRead(Reader in)

Creates a buffering character-input stream that uses a default-sized input buffer.

Parameters:

in - A Reader

Method Detail

getBytesRead

public long getBytesRead()

Keep track of bytesread via ReadLine to account for CR-LF in the stream. Does not keep track of position if use methods other than ReadLine. //TODO should override other methods and throw exception or keep track of bytes read

Returns:

read

public int read()
         throws IOException

Reads a single character.

Overrides:

read in class Reader

Returns:

The character read, as an integer in the range 0 to 65535 (0x00-0xffff), or -1 if the end of the stream has been reached

Throws:

IOException - If an I/O error occurs

read

public int read(char[] cbuf,
                int off,
                int len)
         throws IOException

Reads characters into a portion of an array.

This method implements the general contract of the corresponding read method of the Reader class. As an additional convenience, it attempts to read as many characters as possible by repeatedly invoking the read method of the underlying stream. This iterated read continues until one of the following conditions becomes true:

• The specified number of characters have been read,
• The read method of the underlying stream returns -1, indicating end-of-file, or
• The ready method of the underlying stream returns false, indicating that further input requests would block.

If the first read on the underlying stream returns -1 to indicate end-of-file then this method returns -1. Otherwise this method returns the number of characters actually read.

Subclasses of this class are encouraged, but not required, to attempt to read as many characters as possible in the same fashion.

Ordinarily this method takes characters from this stream's character buffer, filling it from the underlying stream as necessary. If, however, the buffer is empty, the mark is not valid, and the requested length is at least as large as the buffer, then this method will read characters directly from the underlying stream into the given array. Thus redundant BufferedReaderBytesReads will not copy data unnecessarily.

Specified by:

read in class Reader

Parameters:

cbuf - Destination buffer

off - Offset at which to start storing characters

len - Maximum number of characters to read

Returns:

The number of characters read, or -1 if the end of the stream has been reached

Throws:

IOException - If an I/O error occurs

readLine

public String readLine()
                throws IOException

Reads a line of text. A line is considered to be terminated by any one of a line feed ('\n'), a carriage return ('\r'), or a carriage return followed immediately by a linefeed.

Returns:

A String containing the contents of the line, not including any line-termination characters, or null if the end of the stream has been reached

Throws:

IOException - If an I/O error occurs

skip

public long skip(long n)
          throws IOException

Skips characters.

Overrides:

skip in class Reader

Parameters:

n - The number of characters to skip

Returns:

The number of characters actually skipped

Throws:

IllegalArgumentException - If n is negative.

IOException - If an I/O error occurs

ready

public boolean ready()
              throws IOException

Tells whether this stream is ready to be read. A buffered character stream is ready if the buffer is not empty, or if the underlying character stream is ready.

Overrides:

ready in class Reader

Throws:

IOException - If an I/O error occurs

markSupported

public boolean markSupported()

Tells whether this stream supports the mark() operation, which it does.

Overrides:

markSupported in class Reader

mark

public void mark(int readAheadLimit)
          throws IOException

Marks the present position in the stream. Subsequent calls to reset() will attempt to reposition the stream to this point.

Overrides:

mark in class Reader

Parameters:

readAheadLimit - Limit on the number of characters that may be read while still preserving the mark. An attempt to reset the stream after reading characters up to this limit or beyond may fail. A limit value larger than the size of the input buffer will cause a new buffer to be allocated whose size is no smaller than limit. Therefore large values should be used with care.

Throws:

IllegalArgumentException - If readAheadLimit is < 0

IOException - If an I/O error occurs

reset

public void reset()
           throws IOException

Resets the stream to the most recent mark.

Overrides:

reset in class Reader

Throws:

IOException - If the stream has never been marked, or if the mark has been invalidated

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in class Reader

Throws:

IOException