package affectors;

import main.Node;
import main.Globals;

/** 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.

<p> <b>Formula</b>
<br>dNODEX/dt = - CMax * SUBSTRATE * ( (ACTIVATOR ^ nu) / ( K ^ nu + ACTIVATOR ^ nu) )

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Substrate [SUBSTRATE]</td><td> The uncleaved Node</td></tr>
<tr><td>Activator [ACTIVATOR]</td><td> The regulator Node which is activating cleavage</td></tr>
<tr><td>Kappa [K_ACTIVATOR_SUBSTRATE]</td><td> The level of the activator at which it acts half-maximally.</td></tr>
<tr><td>nu [nu_ACTIVATOR_SUBSTRATE]</td><td> Cooperativity of the activation term.</td></tr>
<tr><td>CMax [CMax_SUBSTRATE]</td><td> Maximal rate of cleavage.</td></tr>
</table>

<p><b>Usage</b>
<code><font size = "3"><br>&SUBSTRATE
<blockquote>	&CleavageA_IC	SUBSTRATE	ACTIVATOR	K_ACTIVATOR_SUBSTRATE	nu_ACTIVATOR_SUBSTRATE	C_SUBSTRATE
</blockquote>
&endSUBSTRATE</code></font>

*/

public class CleavageA_ICAff extends Affector {	
	/** The level of activator at which the cleavage reaction proceeds half-maximally. */
	int		kappaParam;
	/** The "cooperativity" exponent for activation. */
	int		nuParam;
	/** The maximal rate of cleavage. */
	int		cMaxParam;
	
	static final String		desc = "Intracellular cleavage of a substrate, regulated by an activator; version A for substrate";
	static final String	[]	nodeDescriptions = {"Uncleaved substrate", "Activator of cleavage"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal activity of the activator of cleavage",
										"nu: cooperativity of activating term",
										"Cmax: maximal rate of cleavage"};
	
	public CleavageA_ICAff()	{}

	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)
	{
		kappaParam = param_nums[0];
		nuParam = param_nums[1];
		cMaxParam = param_nums[2];
	}

	public float getValue(Node which_node)	{
		float total_cleaver = Nodes[1].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm = params[cMaxParam] * source * 
					Phi(total_cleaver, params[kappaParam], params[nuParam]);

		return -Globals.characteristicTime * theTerm;
	}
	
	public float getNCValue(Node which_node)  {
		float total_cleaver = Nodes[1].getIntegrationValue();
		float theTerm = params[cMaxParam] * 
					Phi(total_cleaver, params[kappaParam], params[nuParam]);

		return -Globals.characteristicTime * theTerm;
	}
}