Package htsjdk.tribble.readers

Class AsciiLineReader

java.lang.Object
htsjdk.tribble.readers.AsciiLineReader
All Implemented Interfaces:
LocationAware, LineReader, Closeable, AutoCloseable
public class AsciiLineReader extends Object implements LineReader, LocationAware
A simple class that provides readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader.readLine() method should be used in preference to this class (when the LocationAware functionality is not required) because it offers greater performance.

  • Constructor Details

    • AsciiLineReader

      protected AsciiLineReader()

    • AsciiLineReader

      @Deprecated public AsciiLineReader(InputStream is)
      Deprecated.
      8/8/2017 use from(java.io.InputStream)
      Note: This class implements LocationAware, which requires preservation of virtual file pointers on BGZF inputs. However, if the inputStream wrapped by this class is a BlockCompressedInputStream, it violates that contract by wrapping the stream and returning positional file offsets instead.

    • AsciiLineReader

      @Deprecated public AsciiLineReader(PositionalBufferedStream is)
      Deprecated.
      8/8/2017 use from(java.io.InputStream)
      Parameters:
      is - the PositionalBufferedStream input stream to be wrapped

  • Method Details

    • from

      public static AsciiLineReader from(InputStream inputStream)
      Create an AsciiLineReader of the appropriate type for a given InputStream.
      Parameters:
      inputStream - An InputStream-derived class that implements BlockCompressedInputStream or PositionalBufferedStream
      Returns:
      AsciiLineReader that wraps inputStream

    • getPosition

      public long getPosition()
      Description copied from interface: LocationAware
      The current offset, in bytes, of this stream/writer/file. Or, if this is an iterator/producer, the offset (in bytes) of the END of the most recently returned record (since a produced record corresponds to something that has been read already). See class javadoc for more. Note that for BGZF files, this does not represent an actually file position, but a virtual file pointer.
      Specified by:
      getPosition in interface LocationAware
      Returns:
      The position of the InputStream

    • getLineTerminatorLength

      public int getLineTerminatorLength()
      Returns the length of the line terminator read after the last read line. Returns either: -1 if no line has been read 0 after the last line if the last line in the file had no CR or LF line ending 1 if the line ended with CR or LF 2 if the line ended with CR and LF

    • readLine

      @Deprecated public String readLine(PositionalBufferedStream stream) throws IOException
      Deprecated.
      8/8/2017 use from(java.io.InputStream) to create a new AsciiLineReader and readLine()
      Read 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.
      Parameters:
      stream - the stream to read the next line from
      Returns:
      A String containing the contents of the line or null if the end of the stream has been reached
      Throws:
      IOException

    • readLine

      public String readLine() throws IOException
      Same as readLine(PositionalBufferedStream) but uses the stream provided in the constructor
      Specified by:
      readLine in interface LineReader
      Returns:
      The next string, or null when input is exhausted.
      Throws:
      IOException

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface LineReader

    • toString

      public String toString()
      Overrides:
      toString in class Object