package main;

import java.io.*;
import java.awt.*;
import stoppers.SimpleStop;
import affectors.Affector;
import affectors.HeatShockAff;

/**
This class is supposed to be able to conduct experiments on the currently loaded net.
Currently supported experiments are changing the copy number of a particular gene
and doing a heat shock of a particular gene.  In the near future, I'll also add in
putting an alternate promoter onto a gene.
<p>
The experiments are designed to temporarily modify the currently loaded network when
startExperiment is called, and then undo the modifications when stopExperiment is called.
*/
public class Experiment extends Object {
	int						type;
	final	static	int		UNKNOWN = 0, CHANGE_COPY_NUMBER = 1,
							HEAT_SHOCK = 3, ALTERNATE_PROMOTER = 4;
	String					nodeName;
	Model					model;
	public SimpleStop	stopper;
	float					shockTime, shockLength, rate, oldRate;
	boolean				startedShock = false;
	
	public Experiment() {}
	
	public Experiment(Model model, String filename) {
		this.model = model;
		
		try {
			FileInputStream stream = new FileInputStream(filename);
			BetterTokenizer tokenizer = new BetterTokenizer(stream);
			GeneralInput.setupTokenizer(tokenizer);
			loadParameters(tokenizer);
		} catch(Exception e) {
			System.out.println("Error loading experiment:  " + e.toString());
		}
	}
	
	public void init(Model model)  { this.model = model; }
	

	public void startExperiment() {
		switch(type) {
			case UNKNOWN: return;
			case CHANGE_COPY_NUMBER:
				try {
					for(int cell = 0; cell < model.numCells; cell++) {
					// Figure out which param we have to change
						Node node = model.cells[cell].getNode(nodeName);
					
					// Search that node for the production term - NOTE: we assume only 1 production term per node
						int aff = 0;
						while(aff < node.affectors.length && 
								node.affectors[aff].affectorType != Affector.PRODUCTION)
							aff++;
						if(aff == node.affectors.length) return;	// No production term in this one
						
					// For now, don't bother storing the old value cause it'll always be 1
					// just set the new one
						node.affectors[aff].copyNumber = rate;
					}
				} catch(Exception e) {
					System.out.println("There was a problem starting the experiment: " + e.toString());
				}
			break;
			
			case ALTERNATE_PROMOTER:
/*				// Make the new affector which has the alternate promoter
				Affector aff = ???
				for(int cell = 0; cell < initClass.numCells; cell++)
					initClass.cells[cell].addExperimentToNode(nodeName, aff);
*/			break;
			case HEAT_SHOCK: 
				// Make the new affector which has the alternate promoter
				Affector aff = new HeatShockAff(nodeName, shockTime, shockLength);
				for(int cell = 0; cell < model.numCells; cell++)
					model.cells[cell].addExperimentToNode(nodeName, aff);
			break;
		}
	}
	
	public void endExperiment() {
		switch(type) {
			case CHANGE_COPY_NUMBER:
				try {
					for(int cell = 0; cell < model.numCells; cell++) {
					// Figure out which param we have to change
						Node node = model.cells[cell].getNode(nodeName);
					
					// Search that node for the production term - NOTE: we assume only 1 production term per node
						int aff = 0;
						while(aff < node.affectors.length && 
								node.affectors[aff].affectorType != Affector.PRODUCTION)
							aff++;
						if(aff == node.affectors.length) return;	// No production term in this one
						
					// Set value back to 1
						node.affectors[aff].copyNumber = 1f;
					}
				} catch(Exception e) {
					System.out.println("Problem ending experiment: " + e.toString());
				}
			break;
			case HEAT_SHOCK:  case ALTERNATE_PROMOTER:
				for(int i = 0; i < model.numCells; i++)	{
					model.cells[i].clearExperiment();
				}
			break;
		}
	}




	public void loadParameters(BetterTokenizer tokenizer) throws Exception {
		// Go through looking for parameters, and read in each one
		GeneralInput.indent++;
		String info = GeneralInput.findNextIDToken(tokenizer);
		while(!info.equals("endExperiment")) {
			loadParameter(info, tokenizer);
			info = GeneralInput.findNextIDToken(tokenizer);
		}
		GeneralInput.indent--;
		if(type == CHANGE_COPY_NUMBER) rate = rate / 2f;	// To change from copy number
	}
	
	
	// This function figures out what a particular parameter is, and reads it in.
	// Overload this function to add in more parameters specific to a particular
	// iterator, and then from that overloaded function call super.loadParameter()
	// for anything you don't recognize
	protected void loadParameter(String info, BetterTokenizer tokenizer) throws Exception {
		if(info.equals("Type")) {
			tokenizer.nextToken();
			String type_string = tokenizer.sval;
			if(type_string.equals("CopyNumber")) type = CHANGE_COPY_NUMBER;
			else if(type_string.equals("HeatShock")) type = HEAT_SHOCK;
			else if(type_string.equals("AlternatePromoter")) type = ALTERNATE_PROMOTER;
			else type = UNKNOWN;
		}
		else if(info.equals("Node")) { tokenizer.nextToken();  nodeName = tokenizer.sval; }
		else if(info.equals("Rate")) { tokenizer.nextToken();  rate = (int)tokenizer.nval; }
		else if(info.equals("ShockTime")) { tokenizer.nextToken();  shockTime = (float)tokenizer.nval; }
		else if(info.equals("ShockLength")) { tokenizer.nextToken();  shockLength = (float)tokenizer.nval; }
		else if(info.equals("Stopper")) {
			tokenizer.nextToken();
			String stopper_name = tokenizer.sval;
			Class c = Class.forName("stoppers." + stopper_name);
			stopper = (SimpleStop)c.newInstance();
			stopper.init(model);
			stopper.loadParameters(tokenizer);
		}
	}
	

}