/*
* SiteList.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evolution.alignment;
/**
* interface for any list of sites.
*
* @version $Id: SiteList.java,v 1.9 2005/05/24 20:25:55 rambaut Exp $
*
* @author Andrew Rambaut
*/
public interface SiteList extends PatternList {
/**
* @return number of sites
*/
int getSiteCount();
/**
* Gets the pattern of site as an array of state numbers (one per sequence)
* @return the site pattern at siteIndex
*/
int[] getSitePattern(int siteIndex);
/**
* Gets the pattern index at a particular site
* @return the patternIndex
*/
int getPatternIndex(int siteIndex);
/**
* @return the sequence state at (taxon, site)
*/
int getState(int taxonIndex, int siteIndex);
}