LongLineBufferedReader (htsjdk 2.8.1 API)

java.lang.Object
- java.io.Reader
- - htsjdk.tribble.readers.LongLineBufferedReader

All Implemented Interfaces:

Closeable, AutoCloseable, Readable
```
public class LongLineBufferedReader
extends Reader
```
A variant of BufferedReader with improved performance reading files with long lines. This class is almost identical to BufferedReader, but it retains a single line buffer for accumulating characters in a line, and allows its size to grow. Conversely, BufferedReader assumes each new line will be approximately 80 characters and its performance suffers when that is not the case. Unlike BufferedReader, this class is not thread safe.

Field Summary
- Fields inherited from class java.io.Reader
  lock

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`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
  - LongLineBufferedReader
```
public LongLineBufferedReader(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
  - LongLineBufferedReader
```
public LongLineBufferedReader(Reader in)
```
    Creates a buffering character-input stream that uses a default-sized input buffer.
    
    Parameters:
    
    in - A Reader
- Method Detail
  - 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 BufferedReaderTwos 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

Class LongLineBufferedReader

Field Summary

Fields inherited from class java.io.Reader

Constructor Summary

Method Summary

Methods inherited from class java.io.Reader

Methods inherited from class java.lang.Object

Constructor Detail

LongLineBufferedReader

LongLineBufferedReader

Method Detail

read

read

readLine

skip

ready

markSupported

mark

reset

close