ExperimentTarget.java

package org.seqcode.deepseq.experiments;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

/**
 * ExperimentTarget is a collection of ControlledExperiments representing a set of experiments that all share the same experimental target. 
 * 
 * @author Shaun Mahony
 * @version	%I%, %G%
 */
public class ExperimentTarget {
	protected String name;
	protected ExptConfig econfig;
	protected int index;
	protected List<ExperimentCondition> conditions = new ArrayList<ExperimentCondition>();
	protected List<ControlledExperiment> replicates = new ArrayList<ControlledExperiment>();
	protected List<Sample> signalSamples = new ArrayList<Sample>();
	protected List<Sample> controlSamples = new ArrayList<Sample>();
	protected HashMap<ControlledExperiment, Integer> replicateIndex = new HashMap<ControlledExperiment, Integer>();
	protected HashMap<ControlledExperiment, Integer> replicateCondIndex = new HashMap<ControlledExperiment, Integer>();
	protected HashMap<Integer, ControlledExperiment> indexedReplicate = new HashMap<Integer, ControlledExperiment>();
	protected int numReplicates = 0;
		
	public ExperimentTarget(ExptConfig c, int idx, String n, List<ControlledExperiment> reps){
		econfig = c;
		index=idx;
		name = n;
		replicates = reps;
		numReplicates = replicates.size();
		
		int x=0;
		for(ControlledExperiment rep : replicates){
			if(!signalSamples.contains(rep.getSignal()))
				signalSamples.add(rep.getSignal());
			if(!controlSamples.contains(rep.getControl()))
				controlSamples.add(rep.getControl());
			replicateIndex.put(rep, rep.getIndex());
			indexedReplicate.put(rep.getIndex(), rep);
			replicateCondIndex.put(rep, x);
			
			rep.setTarget(this);
			if(rep.getCondition()==null){
				System.err.println("Null condition for replicate: "+rep.getName()+"\nExperimentManager should initialize conditions before targets!");
				System.exit(1);
			}else{
				if(!conditions.contains(rep.getCondition()))
					conditions.add(rep.getCondition());
			}
		}
	}
	
	//Accessors
	public int getIndex(){return index;}
	public String getName(){return name;}
	public List<ExperimentCondition> getTargetConditions(){return conditions;}
	public List<ControlledExperiment> getTargetExperiments(){return replicates;}
	public int getReplicateIndex(ControlledExperiment r){return replicateIndex.get(r);}
	public ControlledExperiment getIndexedReplicate(int id){return indexedReplicate.get(id);}
	
}