/*
* Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 2 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package edu.msu.cme.rdp.unifrac;
import edu.msu.cme.rdp.multicompare.MCSample;
import edu.msu.cme.rdp.multicompare.taxon.MCTaxon;
import edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample;
import java.util.List;
/**
*
* @author fishjord
*/
public class UnifracTaxon extends MCTaxon {
private float bl;
public UnifracTaxon(int taxid, String name, String rank, float bl) {
this(taxid, name, rank, bl, false);
}
public UnifracTaxon(int taxid, String name, String rank, float bl, boolean unclassified) {
super(taxid, name, rank, unclassified);
this.bl = bl;
}
public UnifracTaxon(MCTaxon taxon, float bl) {
this(taxon.getTaxid(), taxon.getName(), taxon.getRank(), bl);
for(MCSample sample : taxon.getSamples()) {
setSampleCount(sample, taxon.getCount(sample));
}
}
public float getBl() {
return bl;
}
public boolean containsSample(MCSample sample) {
return sampleCountMap.containsKey(sample) && sampleCountMap.get(sample)[0] > 0;
}
public void resetSamples() {
sampleCountMap.clear();
}
public void setSampleCount(MCSample sample, double count) {
double[] d = new double[Count_Array_size];
d[0] = count;
sampleCountMap.put(sample, d);
}
public void addSampleCount(MCSample sample, double count) {
double[] d = sampleCountMap.get(sample);
if( d == null){
d = new double[Count_Array_size];
sampleCountMap.put(sample, d);
}
d[0] += count;
}
public void resetSamples(List<UnifracSample> samplePool) {
int sampleCount = sampleCountMap.size();
this.resetSamples();
for(int index = 0;index < sampleCount;index++) {
UnifracSample sample = samplePool.remove(0);
this.addSampleCount(sample.sample, sample.count);
}
}
}