org.snpeff.binseq.coder.Coder 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.binseq.coder;

import java.io.Serializable;

/**
 * Class used to encode & decode sequences into binary and vice-versa
 * They are usually stored in 'long' words
 * 
 * @author pcingola
 */
@SuppressWarnings("serial")
public abstract class Coder implements Serializable {

	public static final int BITS_PER_LONGWORD = 64;
	public static final int BYTES_PER_LONGWORD = 8;

	/**
	 * How many bases can we pack in a word
	 * @return
	 */
	public abstract int basesPerWord();

	/**
	 * Encode a base using a binary representation
	 * @param c
	 * @return
	 */
	public abstract int baseToBits(char c);

	/**
	 * How many bits do we need for each base
	 * @return
	 */
	public abstract int bitsPerBase();

	/**
	 * Decode bits from a given position in a word
	 * @param word
	 * @param pos
	 * @return
	 */
	public abstract int decodeWord(long word, int pos);

	/**
	 * Index of the last base coded in a word
	 * @return
	 */
	public abstract int lastBaseinWord();

	/**
	 * Bitmask for a base in a word
	 * @return
	 */
	public abstract long mask(int baseIndexInWord);

	/**
	 * Encode a quality using a binary representation
	 * @param c
	 * @return
	 */
	public int qualityToBits(int q) {
		return 0;
	}

	/**
	 * Decode a base using a binary representation
	 * @param c
	 * @return
	 */
	public abstract char toBase(int code);

	/**
	 * Decode a base from a given position in a word
	 * @param word
	 * @param pos
	 * @return
	 */
	public abstract char toBase(long word, int pos);

	/**
	 * Decode a quality
	 * @param c
	 * @return
	 */
	public int toQuality(int code) {
		return 0;
	}
}