htsjdk.samtools.util.BufferedLineReader Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.Defaults;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.LineNumberReader;
import java.nio.charset.Charset;
/**
* Implementation of LineReader that is a thin wrapper around BufferedReader. On Linux, this is faster
* than AsciiLineReaderImpl. If you use AsciiLineReader rather than this class, it will detect the OS
* and delegate to the preferred implementation.
*
* @author [email protected]
*/
public class BufferedLineReader extends LineNumberReader implements LineReader {
public BufferedLineReader(final InputStream is) {
this(is, Defaults.NON_ZERO_BUFFER_SIZE);
}
public BufferedLineReader(final InputStream is, final int bufferSize) {
super(new InputStreamReader(is, Charset.forName("UTF-8")), bufferSize);
}
/**
* Returns a {@link BufferedLineReader} that gets its input from a String. No charset conversion
* is necessary because the String is in unicode.
*/
public static BufferedLineReader fromString(final String s) {
return new BufferedLineReader(new ByteArrayInputStream(s.getBytes()));
}
/**
* Read a line and remove the line terminator
*
* @return the line read, or null if EOF has been reached.
*/
@Override
public String readLine() {
try {
return super.readLine();
} catch (IOException e) {
throw new RuntimeIOException(e);
}
}
/**
* Non-destructive one-character look-ahead.
*
* @return If not eof, the next character that would be read. If eof, -1.
*/
@Override
public int peek() {
try {
mark(2); // Two characters required here as the next read will collapse \r\n to a single \n
final int ret = read();
reset();
return ret;
} catch (IOException e) {
throw new RuntimeIOException(e);
}
}
@Override
public void close() {
try {
super.close();
} catch (IOException e) {
throw new RuntimeIOException(e);
}
}
}