/*
* BootstrapPatterns.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 bootstrap replicate patterns
*
* @version $Id: BootstrapPatterns.java,v 1.12 2005/05/24 20:25:55 rambaut Exp $
*
* @author Andrew Rambaut
*/
public class BootstrapPatterns extends ResamplePatterns {
/**
* Constructor
*/
public BootstrapPatterns() {
}
/**
* Constructor
*/
public BootstrapPatterns(SiteList patterns) {
setPatterns(patterns);
}
/**
* Perform a bootstrap resampling of the patterns
*/
public void resamplePatterns() {
int siteCount = patterns.getSiteCount();
int oldPatternCount = patterns.getPatternCount();
patternIndices = new int[oldPatternCount];
weights = new double[oldPatternCount];
int site, pattern;
patternCount = 0;
for (int i = 0; i < siteCount; i++) {
site = MathUtils.nextInt(siteCount);
pattern = patterns.getPatternIndex(site);
int j = 0;
for (j = 0; j < patternCount; j++) {
if (patternIndices[j] == pattern) {
break;
}
}
if (j < patternCount) {
weights[j] += 1.0;
} else {
patternIndices[patternCount] = pattern;
weights[patternCount] = 1.0;
patternCount++;
}
}
}
}