//DARPA Deliverable - NETWORK CLIENT - Calls several agents to implement an intracellular network.
//Author: David Pettigrew		Date: 8. November 2002
//
//This client establishes connections with the OAA host and  issues Prolog-coded requests to Agents.

import com.sri.oaa2.icl.IclList;
import com.sri.oaa2.icl.IclStruct;
import com.sri.oaa2.icl.IclStr;
import com.sri.oaa2.icl.IclTerm;
import com.sri.oaa2.lib.LibOaa;

import java.io.*;
import java.awt.Dimension;

public class NetworkClient {
	static PrintWriter outputAR;  //Declare outputAR to be an output file
	
	private static IclList solveParams0 = new IclList();
	private static IclList solveParams1 = new IclList();
	private static IclList solveParams2 = new IclList();
	private static IclList solveParams3 = new IclList();	
	private static IclList solveParams4 = new IclList();		

    	public static String getAgentAddress(Client client, String agent) throws Exception {
       		IclList res = new IclList();      		       		
        		client.myOaa.oaaSolve(IclTerm.fromString(true, "agent_host(Addr, "+agent+",Host)"), new IclList(), res);   		        		

		if (res.size() == 0) { throw new Exception("Unable to retrieve "+agent+" address using agent_host"); }				
        		String agentAddr = res.getTerm(0).getTerm(0).toString();
       		return agentAddr;
    	}

	public static void main(String[] args) throws Exception
	{
			//long startTime = System.currentTimeMillis();
			//Open output file
		 	openFiles();

			//Set timing variables (all time is in minutes)
			double dt = 0.01;  //integration step size
			int min = (int)(1.0/dt); //min = scaling constant (number of time steps per minute)
			int hour = 60 * min;  //hour = 60 minutes
			int day = 24 * hour;  //hour = 60 minutes			
			double presimulation_time = 20.0*min; //presimulation time to allow dynamic variables to reach equilibrium
			double simulation_time =  100.0*min;  //simulation time after presimulation
			int plot_resolution = min;   //plot-resolution = 1 minute (one data point written to output file every virtual minute)

			Client client = new Client(args);  //Declare client to be object of class Client

			String stimulusAgentAddr = getAgentAddress(client, "simulateStimulus");
			String rateEquationAgentAddr = getAgentAddress(client, "rateEquationActivation");
			String PKAagentAddr = getAgentAddress(client, "simulatePKAactivation");
			String PhosphorylationAgentAddr = getAgentAddress(client, "simulatePhosphorylation");
			String SGRAgentAddr = getAgentAddress(client, "simulateGeneRegulation");	
								
            			//System.out.println("agentAddr = " + agentAddr);
            			//solveParams = (IclList)IclTerm.fromString(true, "[address("+agentAddr+"), direct_connect(true)]");
            			solveParams0.add(new IclStruct("direct_connect", new IclStr("true")));
            			solveParams0.add(new IclStruct("address", IclTerm.fromString(true,stimulusAgentAddr)));
            			solveParams1.add(new IclStruct("direct_connect", new IclStr("true")));
            			solveParams1.add(new IclStruct("address", IclTerm.fromString(true,rateEquationAgentAddr)));
            			solveParams2.add(new IclStruct("direct_connect", new IclStr("true")));
            			solveParams2.add(new IclStruct("address", IclTerm.fromString(true,PKAagentAddr)));      
            			solveParams3.add(new IclStruct("direct_connect", new IclStr("true")));
            			solveParams3.add(new IclStruct("address", IclTerm.fromString(true,PhosphorylationAgentAddr)));  
            			solveParams4.add(new IclStruct("direct_connect", new IclStr("true")));
            			solveParams4.add(new IclStruct("address", IclTerm.fromString(true,SGRAgentAddr)));              			            			      			            			

			client.sendRequest("simulateStimulus(instantiate, input, 0.0, [5.0, 5.0, 1.5,  25.0, 5.0, 1.5,  45.0, 5.0, 1.5,  65.0, 5.0, 1.5, 85.0, 5.0, 1.5])", solveParams0); 
			client.sendRequest("rateEquationActivation(instantiate, cAMP, 1.0, 1.0, 0.0)", solveParams1);
			client.sendRequest("rateEquationActivation(instantiate, phosphatase, 0.5, 1.0, 0.1)", solveParams1);	  //.1, .017		
			client.sendRequest("simulatePKAactivation(instantiate, 'PKA', [0.0025], [10.0, 1.0], [0.0006], [0.0, 0.0, 3.2])", solveParams2);
			client.sendRequest("simulatePhosphorylation(instantiate, 'CREB', 0.005, 0.5, 0.0)", solveParams3);
			client.sendRequest("simulateGeneRegulation(instantiate, 'ApUch', 1.0, [.09], [activation], 0.01, 0.0, 0.0)", solveParams4);				
			

			double InputSolution = 0.0;
			double cAMP = 0.0;
			double phosphatase = 0.1;			
			double PKA = 0.0;
			double CREB = 0.0;
			double ApUch = 0.0;
			double XR = 0.0;
			double XC = 0.0;
			double XRC = 0.0;
			double R = 0.0;
			double RC = 0.0;					
			
			//Main loop
			for (double t = -presimulation_time/min; t <= simulation_time/min; t += dt)
			{
				InputSolution = Double.parseDouble(client.sendRequest("simulateStimulus(nextStimulus, input, InputSolution, InputSlope, "+t+")", 3, solveParams0)); 				
				client.sendRequest("rateEquationActivation(solve, cAMP, "+InputSolution+")", solveParams1); 
				client.sendRequest("rateEquationActivation(solve, phosphatase, "+(InputSolution+0.1)+")", solveParams1);
				
				R = Double.parseDouble(client.sendRequest("simulatePKAactivation(get, 'PKA', R, C, RC, SlopeR, SlopeC, SlopeRC)", 3, solveParams2));
				RC = Double.parseDouble(client.sendRequest("simulatePKAactivation(get, 'PKA', R, C, RC, SlopeR, SlopeC, SlopeRC)", 5, solveParams2));
				XR = -0.014*R*ApUch;
				XC = 0.014*RC*ApUch;
				XRC = -0.014*RC*ApUch;
								
				client.sendRequest("simulatePKAactivation(solve, 'PKA', "+cAMP+", "+XR+", "+XC+", "+XRC+")", solveParams2);
				client.sendRequest("simulatePhosphorylation(solve, 'CREB', "+PKA+", "+phosphatase+")", solveParams3);
				client.sendRequest("simulateGeneRegulation(solve, 'ApUch', ApUchSlope, ["+(CREB*CREB)+"], [1.0])", solveParams4);						

				cAMP = Double.parseDouble(client.sendRequest("rateEquationActivation(integrate, forwardEuler, cAMP, CyclicAMP, "+dt+")", 4, solveParams1));
				phosphatase = Double.parseDouble(client.sendRequest("rateEquationActivation(integrate, forwardEuler, phosphatase, Phosphatase, "+dt+")", 4, solveParams1));				
				PKA = Double.parseDouble(client.sendRequest("simulatePKAactivation(integrate, forwardEuler, 'PKA', R, C, RC, "+dt+")", 5, solveParams2));
				CREB = Double.parseDouble(client.sendRequest("simulatePhosphorylation(integrate, forwardEuler, 'CREB', CREB, "+dt+")", 4, solveParams3));	
				ApUch = Double.parseDouble(client.sendRequest("simulateGeneRegulation(integrate, forwardEuler, 'ApUch', ApUch, "+dt+")", 4, solveParams4));								
					
				//Print results to output files
				if( (t >= 0.0) & (( (int)(t * min) % plot_resolution) == 0) )  outputAR.println(t+", "+((float)(InputSolution))+", "+((float)(cAMP))+", "+((float)(phosphatase))+", "+((float)(PKA))+", "+((float)(CREB))+", "+((float)(ApUch)));
				//System.out.print(".");   //something to watch while simulation proceeds
				//System.out.print(":");
			}

			System.out.println("Simulation Complete....");
			closeFiles(); //Close output files
			//long endTime = System.currentTimeMillis();
			//System.out.println("Total Run Time: "+((endTime - startTime) / 60000)+" min.; "+((long)((endTime - startTime) % 60000) / 1000.0)+" sec.");			
	}

	public static void openFiles() throws IOException {
		File fileAR = new File("Network.txt");
		outputAR = new PrintWriter(new FileWriter(fileAR));
	}

	public static void closeFiles() { outputAR.close(); }
}