package affectors;

import main.Node;
import main.Globals;

/** Use for multiplicative inhibition of transcription. Formula is 1 minus our 
standard activation s-shaped curve, giving an upside-down s-shaped curve (our Psi
function) with a half-maximal inhibition at K and the degree of non-linearity
controlled by nu. This Affector is designed to work inside of a ProductAff. It
inhibits if multiplied by another term - the value of this affector is positive, so
it will not inhibit if you add it to another term.
You should only use this Affector inside of an <a href=EnhancerRegion.html>EnhancerRegion</a>.

<p> <b>Formula</b>
<br>dnodex/dt = INHIBITOR^nu / (K^nu + INHIBITOR^nu)

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Inhibitor [INHIBITOR]</td><td> The inhibitor Node. </td></tr>
<tr><td>Half-maximal inhibition level [K_INHIBITORnodex]</td><td> The concentration of inhibitor at which transcription is reduced by half. </td></tr>
<tr><td>Cooperativity [nu_INHIBITORnodex]</td><td> The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the S-shaped inhibition function. </td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>   &EnhancerRegionAff	H_nodex
<blockquote>	&ProductAff
<blockquote> 		&TxnSiteActivatorAff	ACTIVATOR	K_ACTIVATORnodex	nu_ACTIVATORnodex
				 	&TxnSiteInhibitorAff	INHIBITOR	K_INHIBITORnodex	nu_INHIBITORnodex</blockquote>
				&endProductAff</blockquote>
			  &endEnhancerRegion </blockquote>
&endnodex</font></code>

*/
public class TxnSiteInhibitorAff extends Affector	{		
	/** The level of inhibition at which transcription inhibited half-maximally. */
	int		kParam, 
	/** The "cooperativity" exponent for inhibition. */
			nuParam;

	static final String		desc = "Multiplicative inhibition of transcription - use for multiplying several activators and inhibitor inside Product";
	static final String	[]	nodeDescriptions = {"Inhibitor"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal level of inhibitor",
										"nu: cooperativity of inhibition"};

	public TxnSiteInhibitorAff()	{	}
	
	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.PRODUCTION;
	}

	public void setParameterNumbers(int [] param_nums)
	{
		kParam = param_nums[0];
		nuParam = param_nums[1];
	}
	
	public float getValue(Node which_node)	{
		return Psi(Nodes[0].getIntegrationValue(),params[kParam],params[nuParam]);
	}
}