CytoscapeExport.java

package edu.uconn.tripoint.export;

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

import quin.network.Location;
import edu.uconn.tripoint.graph.Edge;
import edu.uconn.tripoint.graph.Node;
import edu.uconn.tripoint.pathway.Gene;
import edu.uconn.tripoint.pathway.Pathway;
import edu.uconn.tripoint.pathway.PathwayEdge;
import edu.uconn.tripoint.triangulation.TriangulatedGene;

/**
 * 
 * Exports the pathways into a cytoscape format.
 *
 */
public class CytoscapeExport {
	
	/**
	 * 
	 * @param p
	 * @param genes
	 * @param noncoding
	 * @param outdir
	 */
	public void exportToCytoscapeJSON(Pathway p, Map<Gene, TriangulatedGene> genes, Map<Gene, List<Location>> noncoding, String outdir, String prefix){
		Map<Gene, Integer> geneids = new TreeMap<Gene, Integer>();
		int nindex = 0;
		Map<Integer, CytoscapeNode> nl = new TreeMap<Integer, CytoscapeNode>();
		for(Iterator<Node<Gene,PathwayEdge>> it = p.getNodes().iterator(); it.hasNext();){
			Node<Gene,PathwayEdge> next = it.next();
			int curnindex = nindex++;
			Gene curgene = next.getData();
			geneids.put(curgene, curnindex);
			int nccount = 0;
			if(noncoding.get(curgene) != null){
				nccount = noncoding.get(curgene).size();
			}
			nl.put(curnindex,new PathwayGeneCytoscapeNode(curnindex, p.getId(), genes.get(curgene), nccount));
		}
		
		int eindex = 0;
		List<CytoscapeEdge> el = new LinkedList<CytoscapeEdge>();
		for(Iterator<Edge<Gene,PathwayEdge>> it = p.getEdges().iterator(); it.hasNext();){
			Edge<Gene,PathwayEdge> edge = it.next();
			Gene src = edge.getSource().getData();
			Gene dest = edge.getDestination().getData();
			String type = getStringType(edge.getData().getType());
			el.add(new PathwayCytoscapeEdge(eindex, nl.get(geneids.get(src)), nl.get(geneids.get(dest)), type));
		}
		
		for(Iterator<Gene> git = geneids.keySet().iterator(); git.hasNext();){
			Gene next = git.next();
			List<Location> l = noncoding.get(next);
			if(l != null){
				for(Iterator<Location> lit = l.iterator(); lit.hasNext();){
					int curnindex = nindex++;
					CytoscapeNode n = new NonCodingCytoscapeNode(curnindex, lit.next());
					nl.put(curnindex,n);
					el.add(new PathwayCytoscapeEdge(eindex++, nl.get(geneids.get(next)), n, "NonCoding"));
				}
			}
		}
		
		String outdir2 = outdir;
		if(!outdir.endsWith("/")){
			outdir2 += "/";
		}
		
		String filename = p.getId();
		filename = filename.substring(filename.indexOf(":")+1).replaceAll("[^A-Za-z0-9]", "");
		filename = filename.substring(0, Math.min(filename.length(), 16));
		
		try {
			writeJSONFile(outdir2+prefix+"_"+filename+".json", p, nl, el);
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	
	private String getStringType(int type){
		if(type == PathwayEdge.ACTIVATION){
			return "Activation";
		}
		else if(type == PathwayEdge.INHIBITION){
			return "Inhibition";
		}
		else{
			return "Association";
		}
	}
	
	private void writeJSONFile(String outfile, Pathway p, Map<Integer, CytoscapeNode> nodes, List<CytoscapeEdge> edges) throws IOException{
		BufferedWriter bw  = new BufferedWriter(new FileWriter(outfile));
		bw.write("{\n");
		bw.write("\"data\": {\"name\": \""+p.getId()+"\"},\n");
		bw.write("\"elements\" : {\n");
		bw.write("\"nodes\" : [");
		Iterator<CytoscapeNode> it = nodes.values().iterator();
		if(it.hasNext()){
			bw.write(it.next().toJSON()+"\n");
		}
		while(it.hasNext()){
			bw.write(","+it.next().toJSON()+"\n");
		}
		bw.write("],\n");
		bw.write("\"edges\" : [\n");
		Iterator<CytoscapeEdge> ite = edges.iterator();
		if(ite.hasNext()){
			bw.write(ite.next().toJSON()+"\n");
		}
		while(ite.hasNext()){
			bw.write(","+ite.next().toJSON()+"\n");
		}
		bw.write("]\n");
		bw.write("}\n");
		bw.write("}\n");
		bw.flush();
		bw.close();
	}
	
}