PathwayGeneCytoscapeNode.java

package edu.uconn.tripoint.export;

import edu.uconn.tripoint.triangulation.TriangulatedGene;

public class PathwayGeneCytoscapeNode extends CytoscapeNode {

	private String _pathway;
	private TriangulatedGene _tg;
	private int _noncodingcount;
	
	public PathwayGeneCytoscapeNode(int id, String pathway, TriangulatedGene tg, int nccount){
		super(id);
		_pathway = pathway;
		_tg = tg;
		_noncodingcount = nccount;
	}
	
	@Override
	public String toJSON(){
		StringBuilder sb = new StringBuilder();
		sb.append("{\n");
		sb.append("\"data\" : {\n");
		sb.append("\"id\" : \""+getId()+"\",\n");
		sb.append("\"type\" : \"Pathway Gene\",\n");
		sb.append("\"name\" : \""+_tg.getGene().getId()+"\",\n");
		sb.append("\"pathway\" : \""+_pathway+"\",\n");
		sb.append("\"expression\" : "+_tg.getGene().getValue()+",\n");
		sb.append("\"inconsistency\" : "+_tg.getInconsistencyScore(_pathway)+",\n");
		sb.append("\"inconsistency_pval\" : "+_tg.getInconsistencyPValue(_pathway)+",\n");
		sb.append("\"inconsistency_qval\" : "+_tg.getInconsistencyFDR(_pathway)+",\n");
		sb.append("\"support\" : "+_tg.getSupportScore(_pathway)+",\n");
		sb.append("\"support_pval\" : "+_tg.getSupportPValue(_pathway)+",\n");
		sb.append("\"support_qval\" : "+_tg.getSupportFDR(_pathway)+",\n");
		sb.append("\"consistency\" : "+_tg.getConsistencyScore(_pathway)+",\n");
		sb.append("\"consistency_pval\" : "+_tg.getConsistencyPValue(_pathway)+",\n");
		sb.append("\"consistency_qval\" : "+_tg.getConsistencyFDR(_pathway)+",\n");
		sb.append("\"impact\" : "+_tg.getImpactScore(_pathway)+",\n");
		sb.append("\"impact_pval\" : "+_tg.getImpactPValue(_pathway)+",\n");
		sb.append("\"impact_qval\" : "+_tg.getImpactFDR(_pathway)+",\n");
		sb.append("\"noncoding_count\" : "+_noncodingcount+"\n");
		sb.append("}\n");
		sb.append("}\n");
		return sb.toString();
	}
	
}