/*
* 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.classifier.ClassificationResult;
import edu.msu.cme.rdp.multicompare.MCSample;
import edu.msu.cme.rdp.taxatree.UnifracTree;
import edu.msu.cme.rdp.taxatree.VisitInfo;
import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
import edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder;
import edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder.ClassifierTaxonFactory;
import java.util.List;
import java.util.Map;
/**
*
* @author fishjord
*/
public class UnifracTreeBuilder {
public static class UnifracSample {
public MCSample sample;
public double count;
}
private ClassifierTreeBuilder builder;
public UnifracTreeBuilder(List<ClassificationResult> classifications, final Map<String, UnifracSample> sampleMap) {
this(classifications, sampleMap, 0.0f);
}
public UnifracTreeBuilder(List<ClassificationResult> classifications, final Map<String, UnifracSample> sampleMap, float cutoff) {
builder = new ClassifierTreeBuilder(new UnifracTree(), classifications, cutoff, new ClassifierTaxonFactory<UnifracTaxon>() {
public UnifracTaxon buildTaxon(int taxid, String name, String rank, float conf, boolean unclassified) {
float dist = 1f;
if(rank.equals("sequence"))
dist = 0.0f;
return new UnifracTaxon(taxid, name, rank, dist, unclassified);
}
});
builder.getRoot().topDownVisit(new TreeVisitor<UnifracTaxon>(){
public boolean visitNode(VisitInfo<UnifracTaxon> visitInfo) {
UnifracTaxon taxon = visitInfo.getTaxon();
if(sampleMap.containsKey(taxon.getName()))
taxon.setSampleCount(sampleMap.get(taxon.getName()).sample, sampleMap.get(taxon.getName()).count);
return true;
}
});
((UnifracTree)builder.getRoot()).refreshInnerTaxa();
}
public UnifracTree getUnifracTree() {
return (UnifracTree)builder.getRoot();
}
}