NonCodingTargetExport.java

package edu.uconn.tripoint.export;

import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import quin.network.Location;
import edu.uconn.tripoint.pathway.Gene;
import edu.uconn.tripoint.pathway.Pathway;
import edu.uconn.tripoint.triangulation.TriangulatedGene;

public class NonCodingTargetExport {

	public void ExportNonCodingTargets(Pathway globalpathway, Pathway[] pathways, Collection<TriangulatedGene> genes, Map<Gene, List<Location>> noncoding, String outdir, String prefix) throws IOException{
		String outdir2 = outdir;
		if(!outdir.endsWith("/")){
			outdir2 += "/";
		}
		
		BufferedWriter bw = new BufferedWriter(new FileWriter(outdir2+prefix+"_noncoding.txt"));
		bw.write("Gene ID"+"\t"+
				"Chr"+"\t"+"Start"+"\t"+"End"+"\n");
		for(Iterator<TriangulatedGene> it = genes.iterator(); it.hasNext();){
			TriangulatedGene next = it.next();
			writeLine(bw,next, noncoding);
		}

		bw.flush();
		bw.close();
	}
	
	private void writeLine(BufferedWriter bw, TriangulatedGene g, Map<Gene, List<Location>> noncoding) throws IOException{
		Gene gene = g.getGene();
		List<Location> nc = noncoding.get(gene);
		if(nc.size() > 0){
			String id = gene.getId();
			for(Iterator<Location> it = nc.iterator(); it.hasNext();){
				Location next = it.next();
				bw.write(id+"\t"+
						next.getChr()+"\t"+next.getStart()+"\t"+next.getEnd()+"\n");
			}

		}
	}
}