/*
* JackknifePatterns.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.alignment;
import dr.math.MathUtils;
/**
* Provides 50% jackknife replicate patterns
*
* @version $Id: JackknifePatterns.java,v 1.8 2005/05/24 20:25:55 rambaut Exp $
*
* @author Andrew Rambaut
*/
public class JackknifePatterns extends ResamplePatterns
{
/**
* Constructor
*/
public JackknifePatterns() {
}
/**
* Constructor
*/
public JackknifePatterns(SiteList patterns) {
setPatterns(patterns);
}
/**
* Perform a jackknife resampling of the patterns
*/
public void resamplePatterns() {
int siteCount = patterns.getSiteCount();
int oldPatternCount = patterns.getPatternCount();
int[] siteIndices = MathUtils.shuffled(siteCount);
int n = siteCount / 2;
patternIndices = new int[oldPatternCount];
weights = new double[oldPatternCount];
int pattern;
patternCount = 0;
for (int i = 0; i < n; i++) {
pattern = patterns.getPatternIndex(siteIndices[i]);
int j = 0;
for (j = 0; j < patternCount; j++) {
if (patternIndices[j] == pattern) {
break;
}
}
if (j < patternCount) {
weights[j] += 1.0;
} else {
patternIndices[j] = pattern;
weights[j] = 1.0;
patternCount++;
}
}
}
}