/*
* SiteLogLikelihoodLogger.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.app.beagle.tools;
import dr.evomodel.treelikelihood.BeagleTreeLikelihood;
import dr.inference.loggers.LogColumn;
import dr.inference.loggers.Loggable;
import dr.inference.loggers.NumberColumn;
import dr.xml.Reportable;
public class SiteLogLikelihoodLogger implements Loggable, Reportable {
BeagleTreeLikelihood beagleTreeLikelihood;
int patternCount;
private SiteLogLikelihoodColumn[] columns = null;
public SiteLogLikelihoodLogger(BeagleTreeLikelihood beagleTreeLikelihood) {
this.beagleTreeLikelihood = beagleTreeLikelihood;
patternCount = beagleTreeLikelihood.getPatternCount();
}// END: Constructor
@Override
public LogColumn[] getColumns() {
if (columns == null) {
columns = new SiteLogLikelihoodColumn[patternCount];
for (int site = 0; site < patternCount; site++) {
columns[site] = new SiteLogLikelihoodColumn(site);
}
}
return columns;
}// END: getColumns
private double getSiteLogLikelihood(int site) {
double[] siteLikelihoods = beagleTreeLikelihood.getSiteLogLikelihoods();
return siteLikelihoods[site];
}// END: getSiteLogLikelihoods
private class SiteLogLikelihoodColumn extends NumberColumn {
final int site;
public SiteLogLikelihoodColumn(int site) {
super("SiteLogLikelihoodColumn");
this.site = site;
}
@Override
public double getDoubleValue() {
return getSiteLogLikelihood(site);
}
}// END: SiteLogLikelihoodColumn class
public String toString() {
StringBuilder sb = new StringBuilder();
for (int site = 0; site < patternCount; ++site) {
if (site > 0) {
sb.append(", ");
}
sb.append(getColumns()[site].getFormatted());
}
return sb.toString();
}// END: toString
@Override
public String getReport() {
return toString();
}// END: getReport
}// END: class