Package 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:

  • Field Summary

    Fields inherited from class java.io.Reader

    lock

  • Constructor Summary

    Constructors
    Constructor
    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
    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

    nullReader, read, read, transferTo

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • 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 Details

    • 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 AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in class Reader
      Throws:
      IOException