package affectors;

import main.Node;
import main.Globals;

/**Diploid version of CleaveageA_ICAff.  Reduces to same result if the two alleles are
 * identical.  Assumptions for diploidizing: (1) Two alleles catalyze reactions instantly
 * so there's no chance that one allele is able to bind and not cleave (thus inhibiting
 * the other).  (2) There is no synergy or cooperativity between the two (i.e. the two
 * alleles don't see each other or interact) and the total activity is simply the sum of
 * the individual activities.  It would be interesting to compare this
 * where the nonlinearity depends on some function of the sum of the concentrations
 *
 * <p>This is one half of an affector that cleaves a single node into two other
 * nodes. The rate of cleavage is regulated by a separate activator node (an enzyme).
 * Use this affector in the uncleaved species.  Use the B version in each
 * of the product species.
 *
 * <br>dNODEX/dt = -0.5*SUBSTRATE(CMax1 * ( (ACTIVATOR1 ^ nu1) / ( K1 ^ nu1 + ACTIVATOR1 ^ nu1) )+
 * CMax2 * ( (ACTIVATOR2 ^ nu2) / ( K2 ^ nu2 + ACTIVATOR2 ^ nu2) )
 *
 * <p> <b>Parameters</b>
 * <table width="500" border="1">
 * <tr><td width="150">Substrate [SUBSTRATE]</td><td> The uncleaved Node</td></tr>
 * <tr><td>Activator1 [ACTIVATOR1]</td><td> The regulator Node allele 1 which is activating cleavage</td></tr>
 * <tr><td>Activator1 [ACTIVATOR1]</td><td> The regulator Node allele 2 which is activating cleavage</td></tr>
 * <tr><td>Kappa1 [K_ACTIVATOR1_SUBSTRATE]</td><td> The level of the activator allele 1 at
 * which it acts half-maximally.</td></tr>
 * <tr><td>Kappa2 [K_ACTIVATOR2_SUBSTRATE]</td><td> The level of the activator allele 2 at
 * which it acts half-maximally.</td></tr>
 * <tr><td>nu1 [nu_ACTIVATOR1_SUBSTRATE]</td><td> Cooperativity of the activation allele 1.</td></tr>
 * <tr><td>nu2 [nu_ACTIVATOR2_SUBSTRATE]</td><td> Cooperativity of the activation allele 2.</td></tr>
 * <tr><td>CMax1 [CMax1_SUBSTRATE]</td><td> Maximal rate of cleavage for allele 1.</td></tr>
 * <tr><td>CMax2 [CMax2_SUBSTRATE]</td><td> Maximal rate of cleavage for allele 2.</td></tr>
 * </table>
 *
 * <p><b>Usage</b>
 * <code><font size = "3"><br>&CLEAVED_NODE
 * <blockquote>	&CleavageB_IC	SUBSTRATE 	ACTIVATOR1 	ACTIVATOR2	K_ACTIVATOR1_SUBSTRATE
 * K_ACTIVATOR2_SUBSTRATE 	nu_ACTIVATOR1_SUBSTRATE		nu_ACTIVATOR2_SUBSTRATE 	C1_SUBSTRATE 	C2_SUBSTRATE
 * </blockquote>
 * &endCLEAVED_NODE</code></font>
 */

public class CleavageA_ICDipAff extends Affector {
	/** The level of activator allele 1 at which the cleavage reaction proceeds half-maximally. */
	int		kappaParam1;
	/** The level of activator allele 2 at which the cleavage reaction proceeds half-maximally. */
	int		kappaParam2;
	/** The "cooperativity" exponent for activation of allele 1. */
	int		nuParam1;
	/** The "cooperativity" exponent for activation of allele 2. */
	int		nuParam2;
	/** The maximal rate of cleavage of allele 1. */
	int		cMaxParam1;
		/** The maximal rate of cleavage of allele 2. */
	int		cMaxParam2;

	
	static final String		desc = "Diploid Intracellular cleavage of a substrate, regulated by an activator; version A for substrate";
	static final String	[]	nodeDescriptions = {"Uncleaved substrate",
												"Activator of cleavage allele 1",
												"Activator of cleavage allele 2"};
	static final String	[]	paramDescriptions ={"Kappa: half-maximal activity of the activator of cleavage allele 1",
												"Kappa: half-maximal activity of the activator of cleavage allele 2",
												"nu: cooperativity of activating allele 1",
												"nu: cooperativity of activating allele 2",
												"Cmax: maximal rate of cleavage allele 1",
												"Cmax: maximal rate of cleavage allele 2"};
	
	public CleavageA_ICDipAff()	{}

	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, nodeDescriptions, paramDescriptions);
		setContainsTarget(true);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.GG;
		this.Type[TERMTYPE] = Affector.CONVERSION;
	}
	
	
	public void setParameterNumbers(int [] param_nums)
	{
		kappaParam1 = param_nums[0];
		kappaParam2 = param_nums[1];
		nuParam1 = param_nums[2];
		nuParam2 = param_nums[3];
		cMaxParam1 = param_nums[4];
		cMaxParam2 = param_nums[5];
	}

	public float getValue(Node which_node)	{
		float total_cleaver1 = Nodes[1].getIntegrationValue();
		float total_cleaver2 = Nodes[2].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm1 = params[cMaxParam1] * source *
					Phi(total_cleaver1, params[kappaParam1], params[nuParam1]);
		float theTerm2 = params[cMaxParam2] * source *
					Phi(total_cleaver2, params[kappaParam2], params[nuParam2]);


		return -0.5f*Globals.characteristicTime * (theTerm1+theTerm2);
	}
	
	public float getNCValue(Node which_node)  {
		float total_cleaver1 = Nodes[1].getIntegrationValue();
		float total_cleaver2 = Nodes[2].getIntegrationValue();
		float theTerm1 = params[cMaxParam1] *
					Phi(total_cleaver1, params[kappaParam1], params[nuParam1]);
		float theTerm2 = params[cMaxParam2] *
					Phi(total_cleaver2, params[kappaParam2], params[nuParam2]);


		return -0.5f*Globals.characteristicTime * (theTerm1+theTerm2);
	}
}