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package net.sf.samtools.util;

import java.io.IOException;
import java.io.InputStream;

/**
 * This is the old AsciiLineReader, except that lineBuffer is stored as chars rather than bytes.  It appears
 * that the String ctor that takes byte[] is significantly slower than the one that takes char[].
 *
 * Note that in general in Picard, conversion between ASCII bytes and chars is encapsulated in StringUtil.
 * This class is an exception because there are significant performance implications.  It simply casts bytes
 * to chars.
 *
 * On some platforms (e.g. Linux), BufferedLineReader is faster than this class.  If you use AsciiLineReader
 * instead of this class, it will detect the OS and delegate to the preferred implementation for that platform.
 *
 * @author alecw@broadinstitute.org
 */
public class AsciiLineReaderImpl implements LineReader {

    private static final char LINEFEED = '\n';
    private static final char CARRIAGE_RETURN = '\r';
    private final InputStream is;
    private byte[] buffer;
    private int nextChar;
    private int nChars;
    // Allocate this only once, despite the fact that it is essentially a local variable of readLine()
    private char[] lineBuffer = new char[10000];
    private int lineNumber = 0;

    /**
     * Prepare to read lines from the given input stream, with default buffer size
     * @param is need not be buffered, because this class does buffered reading
     */
    public AsciiLineReaderImpl(final InputStream is) {
        this(is, 512000);
    }

    /**
     * Prepare to read lines from the given input stream
     * @param is need not be buffered, because this class does buffered reading
     * @param bufferSize
     */
    public AsciiLineReaderImpl(final InputStream is, final int bufferSize) {
        this.is = is;
        buffer = new byte[bufferSize];
        nextChar = nChars = 0;
    }

    /**
     * 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.
     *
     * @return     A String containing the contents of the line or null if the
     *             end of the stream has been reached.  Terminator is not included in
     *             the returned string.
     */
    public String readLine() {
        return readLine(false);
    }

    /**
     * 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.
     *
     * @param      includeTerminators  If true, the line-termination characters
     *             are included in the returned string.
     *
     * @return     A String containing the contents of the line or null if the
     *             end of the stream has been reached
     */
    public String readLine(final boolean includeTerminators) {
        int linePosition = 0;

        while (true) {
            if (nChars == -1) {
                return null;
            }

            // Refill buffer if neccessary
            if (nextChar == nChars) {
                fill();
                if (nextChar == nChars || nChars == -1) {
                    // eof reached.  Return the last line, or null if this is a new line
                    if (linePosition > 0) {
                        ++lineNumber;
                        return new String(lineBuffer, 0, linePosition);
                    } else {
                        return null;
                    }
                }
            }


            final char c = (char) (buffer[nextChar++] & 0xFF);
            if (c == LINEFEED || c == CARRIAGE_RETURN) {

                if (includeTerminators) {
                    lineBuffer[linePosition++] = c;
                    if (c == CARRIAGE_RETURN && peek() == LINEFEED) {
                        lineBuffer[linePosition++] = c;
                        nextChar++; // <= to account for the '\n' we just ate
                    }
                } else {
                    if (c == CARRIAGE_RETURN && peek() == LINEFEED) {
                        nextChar++; // <= skip the trailing \n in case of \r\n termination
                    }

                }
                ++lineNumber;
                return new String(lineBuffer, 0, linePosition);
            } else {
                // Expand line buffer size if neccessary.  Reservce at least 2 characters
                // for potential line-terminators in return string

                if (linePosition > (lineBuffer.length - 3)) {
                    final char[] temp = new char[lineBuffer.length + 1000];
                    System.arraycopy(lineBuffer, 0, temp, 0, lineBuffer.length);
                    lineBuffer = temp;
                }

                lineBuffer[linePosition++] = c;
            }
        }
    }

    /**
     * @return the line number of the most recently read line.  After reading the first line, this method
     * return 1.
     */
    public int getLineNumber() {
        return lineNumber;
    }

    /**
     * Peek ahead one character, filling from the underlying stream if neccessary.
     *
     * @return peeked character.
     * @throws java.io.IOException
     */
    public int peek() {
        // Refill buffer if neccessary
        if (nextChar == nChars) {
            fill();
            if (nextChar == nChars) {
                // eof reached.
                return -1;
            }
        }
        return buffer[nextChar];

    }

    private void fill() {
        try {
            nChars = is.read(buffer);
            nextChar = 0;
        } catch (IOException e) {
          //  throw new RuntimeIOException(e);
        }
    }

    public void close() {
        try {
            is.close();
        } catch (IOException e) {
            // Ignore exception
        }
    }
}
