/*
* PartitionedTreeLogger.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.evomodel.epidemiology.casetocase;
import dr.evolution.tree.*;
import dr.evomodel.tree.TreeLogger;
import dr.inference.loggers.LogFormatter;
import java.text.NumberFormat;
/**
* Logs a partitioned tree. Breaks branches in two at infection times and adds a node of degree 2.
* TreeAnnotator won't work.
*
* @author Matthew Hall
*/
public class PartitionedTreeLogger extends TreeLogger {
CaseToCaseTreeLikelihood c2cTL;
Tree originalTree;
private LogUpon condition = null;
private TreeTraitProvider.Helper treeTraitHelper;
public PartitionedTreeLogger(CaseToCaseTreeLikelihood c2cTL, Tree tree, BranchRates branchRates,
TreeAttributeProvider[] treeAttributeProviders,
TreeTraitProvider[] treeTraitProviders,
LogFormatter formatter, int logEvery, boolean nexusFormat,
boolean sortTranslationTable, boolean mapNames, NumberFormat format,
TreeLogger.LogUpon condition) {
super(tree, branchRates, treeAttributeProviders, treeTraitProviders, formatter, logEvery, nexusFormat,
sortTranslationTable, mapNames, format, condition);
this.c2cTL = c2cTL;
this.originalTree = tree;
this.condition = condition;
}
public void log(long state){
final boolean doIt = condition != null ? condition.logNow(state) :
(logEvery < 0 || ((state % logEvery) == 0));
if(!doIt)
return;
setTree(c2cTL.addTransmissionNodes(originalTree));
super.log(state);
}
}