/*
* HiddenCodons.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.datatype;
/**
* @author Marc A. Suchard
*/
public class HiddenCodons extends Codons implements HiddenDataType {
public static final String DESCRIPTION = "hiddenCodon";
public static final HiddenCodons UNIVERSAL_HIDDEN_2 = new HiddenCodons(GeneticCode.UNIVERSAL,2);
public static final HiddenCodons UNIVERSAL_HIDDEN_3 = new HiddenCodons(GeneticCode.UNIVERSAL,3);
/**
* Private constructor - DEFAULT_INSTANCE provides the only instance
*/
private HiddenCodons(GeneticCode geneticCode, int hiddenClassCount) {
super(geneticCode);
this.hiddenClassCount = hiddenClassCount;
}
/**
* returns an array containing the non-ambiguous states that this state represents.
*/
public boolean[] getStateSet(int state) {
boolean[] stateSet = new boolean[stateCount*hiddenClassCount];
if (!isAmbiguousState(state)) {
for(int h=0; h<hiddenClassCount; h++)
stateSet[h*stateCount + state] = true;
} else {
for (int i = 0; i < stateCount; i++) {
stateSet[i] = true;
}
}
return stateSet;
}
public int getStateCount() {
return stateCount*hiddenClassCount;
}
private int hiddenClassCount;
public int getHiddenClassCount() {
return hiddenClassCount;
}
}