// Alignment.java
//
// (c) 1999-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)


package pal.alignment;

import java.io.*;

import pal.datatype.*;
import pal.misc.*;


/**
 * interface for any alignment data.
 *
 * @version $Id: Alignment.java,v 1.15 2003/03/23 00:12:57 matt Exp $
 *
 * @author Alexei Drummond
 * @author Korbinian Strimmer
 * @note Removed setDataType(), setFrequencies(), and getFrequencies() from interface
 * As they seem better placed in concrete implementations only and should not be a requirement of an alignment, or in the case of Frequencies, can be
 * found using Alignment.Utils.estimateFrequencies(Alignment)
 */
public interface Alignment extends Serializable, IdGroup
{
	//
	// Public stuff
	//

	/** character used to designate gaps */
	static char GAP = DataType.PRIMARY_SUGGESTED_GAP_CHARACTER;

	/** character used to designate unknown characters */
	static char UNKNOWN = DataType.UNKNOWN_CHARACTER;
	/** character used to designate unknown characters */
	static String UNKNOWN_TLA = DataType.UNKNOWN_TLA;

	/**
	 * A three letter acronym version of a gap.
	 */
	static String GAP_TLA = ""+GAP+GAP+GAP;


	/** Characters that might be used as gaps */
	static String GAPS = "_-?.";

	// Abstract method

	/** sequence alignment at (sequence, site) */
	char getData(int seq, int site);

		/**
	 * @return number of sites for each sequence in this alignment
	 */
	int getSiteCount();

	/**
	 * Return number of sequences in this alignment
	 */
	int getSequenceCount();

	/**
	 * Return DataType of this alignment.
	 */
	DataType getDataType();

	/**
	 * Returns string representation of single sequence in
	 * alignment with gap characters included.
	 */
	String getAlignedSequenceString(int sequence);


}