/*
* 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.multicompare.visitors;
import edu.msu.cme.rdp.multicompare.MCSample;
import edu.msu.cme.rdp.multicompare.taxon.MCTaxon;
import edu.msu.cme.rdp.taxatree.VisitInfo;
import edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor;
import java.io.PrintStream;
import java.util.List;
/**
*
* @author fishjord
*/
public class EstimateSPrintVisitor implements TreeVisitor<MCTaxon> {
private PrintStream out;
private List<MCSample> samples;
private String rank;
private int nodeCount = 0;
public EstimateSPrintVisitor(PrintStream out, List<MCSample> samples, String rank, int nodeCount) {
this.out = out;
this.samples = samples;
this.rank = rank;
this.nodeCount = nodeCount;
printHeader();
}
private void printHeader() {
out.println("EstimateS File prepared by RDP MultiCompare Library Comparision Tool");
out.println(nodeCount + "\t" + samples.size());
}
public boolean visitNode(VisitInfo<MCTaxon> info) {
MCTaxon taxon = info.getTaxon();
if(!taxon.getRank().equals(rank))
return true;
StringBuffer sampleBuf = new StringBuffer();
int seqCount = 0;
for(MCSample sample : samples) {
sampleBuf.append(taxon.getCount(sample) + "\t");
seqCount += taxon.getCount(sample);
}
if(seqCount > 0)
out.println(sampleBuf);
return true;
}
}