/*
* HiddenLinkageLogger.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.tree;
import dr.inference.loggers.LogFormatter;
import dr.inference.loggers.MCLogger;
/**
* @author Aaron Darling
*/
public class HiddenLinkageLogger extends MCLogger {
HiddenLinkageModel hlm;
public HiddenLinkageLogger(HiddenLinkageModel hlm, LogFormatter formatter, int logEvery)
{
super(formatter, logEvery, false);
this.hlm = hlm;
}
public void startLogging() {
String[] labels = new String[1 + hlm.getData().getReadsTaxa().getTaxonCount()];
labels[0] = "iter";
for(int i=1; i<labels.length; i++){
labels[i] = hlm.getData().getReadsTaxa().getTaxonId(i-1);
}
this.logLabels(labels);
}
public void log(long state) {
if(state % logEvery != 0)
return;
String[] values = new String[1 + hlm.getData().getReadsTaxa().getTaxonCount()];
values[0] = new Long(state).toString();
for(int i=1; i<values.length; i++){
values[i] = new Integer(hlm.getLinkageGroupId(hlm.getData().getReadsTaxa().getTaxon(i-1))).toString();
}
this.logValues(values);
}
}