ControlledExperiment.java

package org.seqcode.deepseq.experiments;


/**
 * ControlledExperiment combines two Samples representing signal and control experiments. 
 * An object of this type may be considered as a single replicate of a given ExperimentCondition.
 * Maintains traceback links to parent conditions, targets, and experiment types.
 * 
 * @author Shaun Mahony
 * @version	%I%, %G%
 */
public class ControlledExperiment {

	protected ExptConfig econfig;
	protected int index;
	protected Sample signal=null; 	//signal channel
	protected Sample control=null;	//control channel
	protected double ctrlScalingRatio = 1.0; //scaling signal channel versus control channel
	protected double signalVsNoiseFraction= 0.0; //Fraction of reads assigned to signal in the signal channel. Init to zero to parameterize Poisson background model in the absence of a sig/noise estimate
	protected String condName;
	protected String repName;
	protected String name;
	protected ExperimentCondition myCondition=null;
	protected ExperimentTarget myTarget = null;
	protected ExperimentType myExptType= null;
	
	public ControlledExperiment(ExptConfig c, int idx, String cn, String rn, Sample sig, Sample ctrl){
		econfig = c;
		index=idx;
		condName = cn;
		repName = rn;
		name = condName+":"+repName;
		signal=sig;
		control = ctrl;
		
		//Initialize with read count normalization. 
		//Other scaling strategies (median, regression, SES) will be initialized in ExperimentCondition
		ctrlScalingRatio = control!=null ? (signal.getHitCount()/control.getHitCount())*econfig.getFixedScalingFactor() : 1;
		
		//Start with assumption of no signal
		signalVsNoiseFraction = 0.0;
	}
	
	//Accessors
	public int getIndex(){return index;}
	public String getName(){return name;}
	public String getCondName(){return condName;}
	public String getRepName(){return repName;}
	public Sample getSignal(){return signal;}
	public Sample getControl(){return control;}
	public boolean hasControl(){return control!=null;}
	public double getControlScaling(){return ctrlScalingRatio;}
	public double getSignalVsNoiseFraction(){return signalVsNoiseFraction;}
	public void setSignalVsNoiseFraction(double snf){signalVsNoiseFraction=snf;}
	public ExperimentCondition getCondition(){return myCondition;}
	public ExperimentTarget getTarget(){return myTarget;}
	public ExperimentType getExptType(){return myExptType;}
	
	public void setScaling(double s){ctrlScalingRatio = s;}
	public void setCondition(ExperimentCondition c){myCondition = c;}
	public void setTarget(ExperimentTarget t){myTarget = t;}
	public void setExptType(ExperimentType t){myExptType = t;}
	
		
}