/*
* AlloppSequenceReassignment.java
*
* Copyright (c) 2002-2017 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.evomodel.alloppnet.operators;
import dr.evolution.util.Taxon;
import dr.evomodel.alloppnet.speciation.AlloppLeggedTree;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesNetworkModel;
import dr.evomodel.alloppnet.parsers.AlloppSequenceReassignmentParser;
import dr.inference.operators.SimpleMCMCOperator;
import dr.math.MathUtils;
import java.util.ArrayList;
/**
*
* @author Graham Jones
* Date: 01/07/2011
*/
public class AlloppSequenceReassignment extends SimpleMCMCOperator {
private final AlloppSpeciesNetworkModel apspnet;
private final AlloppSpeciesBindings apsp;
public AlloppSequenceReassignment(AlloppSpeciesNetworkModel apspnet, AlloppSpeciesBindings apsp, double weight) {
this.apspnet = apspnet;
this.apsp = apsp;
setWeight(weight);
}
public String getPerformanceSuggestion() {
return "None";
}
@Override
public String getOperatorName() {
return AlloppSequenceReassignmentParser.SEQUENCE_REASSIGNMENT + "(" + apspnet.getId() +
"," + apsp.getId() + ")";
}
@Override
public double doOperation() {
apspnet.beginNetworkEdit();
if (MathUtils.nextInt(10) == 0) {
int tt = MathUtils.nextInt(apspnet.getNumberOfTetraTrees());
AlloppLeggedTree ttree = apspnet.getTetraploidTree(tt);
ArrayList<Taxon> sptxs = ttree.getSpeciesTaxons();
for (Taxon tx : sptxs) {
int spi = apsp.apspeciesId2index(tx.getId());
apsp.flipAssignmentsForAllGenesOneSpecies(spi);
}
apspnet.flipLegsOfTetraTree(tt);
} else {
if (MathUtils.nextInt(2) == 0) {
apsp.permuteOneSpeciesOneIndivForOneGene();
} else {
apsp.permuteSetOfIndivsForOneGene();
}
}
apspnet.endNetworkEdit();
assert apspnet.alloppspeciesnetworkOK();
return 0;
}
}