org.snpeff.fileIterator.LineFileIterator Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.fileIterator;

import java.io.IOException;
import java.util.Iterator;

import org.snpeff.util.Gpr;

/**
 * Iterate on each line in this file
 * 
 * @author pcingola
 */
public class LineFileIterator extends FileIterator {

	public static boolean debug = false;

	public LineFileIterator(String lineSeqFileName) {
		super(lineSeqFileName);
		line = null;
		lineNum = 0;
		reader = null;
		reader = Gpr.reader(lineSeqFileName);
	}

	public LineFileIterator(String lineSeqFileName, boolean gzip) {
		super(lineSeqFileName);
		line = null;
		lineNum = 0;
		reader = null;
		reader = Gpr.reader(lineSeqFileName, gzip);
	}

	@Override
	public Iterator iterator() {
		return this;
	}

	/**
	 * Read a sequence from the file
	 * @return
	 */
	@Override
	protected String readNext() {
		try {
			if (reader.ready()) {
				line = reader.readLine(); // Read a line (only if needed)
				if (line != null) {
					lineNum++;
					return line;
				}
			}
		} catch (IOException e) {
			return null;
		}

		return null;
	}
}