/* * HiddenAminoAcids.java * * Copyright (c) 2002-2016 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.datatype; /** * @author Marc A. Suchard */ public class HiddenAminoAcids extends AminoAcids implements HiddenDataType { public static final String DESCRIPTION = "hiddenAminoAcid"; public static final HiddenAminoAcids AMINO_ACIDS_HIDDEN_1 = new HiddenAminoAcids(1); public static final HiddenAminoAcids AMINO_ACIDS_HIDDEN_2 = new HiddenAminoAcids(2); public static final HiddenAminoAcids AMINO_ACIDS_HIDDEN_3 = new HiddenAminoAcids(3); public static final HiddenAminoAcids AMINO_ACIDS_HIDDEN_4 = new HiddenAminoAcids(4); /** * Private constructor - DEFAULT_INSTANCE provides the only instance */ private HiddenAminoAcids(int hiddenClassCount) { super(); this.hiddenClassCount = hiddenClassCount; } /** * returns an array containing the non-ambiguous states that this state represents. */ public boolean[] getStateSet(int state) { return Utils.getStateSet(state, stateCount, hiddenClassCount, AminoAcids.INSTANCE); } public int getStateCount() { return stateCount * hiddenClassCount; } public int getHiddenClassCount() { return hiddenClassCount; } private int hiddenClassCount; }