/*
* 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;
}