package affectors;

import main.Node;
import main.Globals;

/** This is one half of an affector that cleaves a single node into two other
nodes under the influence of an inhibitor.  Use this affector in each of the product species.  
Use the A version in the
uncleaved species.  This one is opposite to the Cleavage_IC affectors in that the regulator
inhibits cleavage rather than activates it.  Otherwise they are identical. 

<p> <b>Formula</b>
<br>dNODEX/dt = CMax * SUBSTRATE * ( 1 - (INHIBITOR ^ nu) / ( K ^ nu + INHIBITOR ^ 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>Inhibitor [INHIBITOR]</td><td> The regulator Node which is inhibiting cleavage</td></tr>
<tr><td>Kappa [K_INHIBITOR_SUBSTRATE]</td><td> The level of the inhibitor at which it acts half-maximally.</td></tr>
<tr><td>nu [nu_INHIBITOR_SUBSTRATE]</td><td> Cooperativity of the inhibitory 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>&CLEAVED_NODE
<blockquote>	&Cleavage2B_IC	SUBSTRATE	INHIBITOR	K_INHIBITOR_SUBSTRATE	nu_INHIBITOR_SUBSTRATE	C_SUBSTRATE
</blockquote>
&endCLEAVED_NODE</code></font>
*/

public class Cleavage2B_ICAff extends Affector {	
	/** The level of inhibitor at which the cleavage reaction proceeds half-maximally. */
	int		kappaParam;
	/** The "cooperativity" exponent for the reaction. */
	int		nuParam;
	/** The maximal rate of cleavage. */
	int		cMaxParam;
		
	static final String		desc = "Intracellular cleavage of a substrate, regulated by an inhibitor; version B for product";
	static final String	[]	nodeDescriptions = {"Uncleaved substrate", "Inhibitor of cleavage"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal activity of the inhibitor of cleavage",
										"nu: cooperativity of inhibitory term",
										"Cmax: maximal rate of cleavage"};
	
	public Cleavage2B_ICAff()	{}

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

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.FF;
		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_inhibitor = Nodes[1].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm = params[cMaxParam] * source * 
					Psi(total_inhibitor, params[kappaParam], params[nuParam]);

		return Globals.characteristicTime * theTerm;
	}
	
}