package affectors;

import main.Node;
import main.Globals;
import main.Cell;

/** Use for activation + inhibition of transcription.  Activates according to an S-shaped function
(Phi function) with a half maximal activation level K and a cooperativity nu.  Inhibits by multiplying
the S-shaped activation function (Phi function) by an upside down-S shaped inhibition function (Psi).
This is identical to what you would get by multiplying Txn1Aff times TxnSiteInhibitorAff, except that
it is designed to work inside of a meta-affector, and models the situation in which the inhibitor
squelches the transcriptional-activating effect independent of activator concentration, rather than
reducing the effectiveness of bound activator (see TxnSiteActInhibitAff for this option) or reducing
the effective concentration of the activator (see TxnSiteActInhibit2Aff for this option).  This
family is designed to work inside of a meta-affector.  You should only use this Affector inside of
an <a href=EnhancerRegion.html>EnhancerRegion</a>.

<p> <b>Formula</b>
<br>inhibit_term = 1 - [(INHIBITOR/K_inhibit)^nu_inhibit * / (1 + (INHIBITOR/K_inhibit)^nu_inhibit)]
<br>dnodex/dt = ((ACTIVATOR/K_act)^nu / (1 + (ACTIVATOR/K)^nu) * inhibit_term

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Activator [ACTIVATOR]</td><td> The transcriptional activator Node</td></tr>
<tr><td width="150">Inhibitor [INHIBITOR]</td><td> The transcriptional inhibitor Node</td></tr>
<tr><td>Half-max activation level of activator [K_ACTIVATORnodex]</td><td> The concentration of activator at which transcription proceeds at half the maximal rate this particular "site" is capable of driving, absent inhibition</td></tr>
<tr><td>Cooperativity of activator [nu_ACTIVATORnodex]</td><td> The non-linearity of the activating function.  The higher the value, the sharper the curves in the S-shaped activation function</td></tr>
<tr><td>Half-max inhibition level of inhibitor [K_INHIBITORnodex]</td><td> The concentration of inhibitor at which transcription proceeds at half its rate without inhibitor</td></tr>
<tr><td>Cooperativity of inhibitor [nu_INHIBITORnodex]</td><td> The non-linearity of the inhibition 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>&EnhancerRegion	H_nodex
<blockquote>   &TxnSiteActivatorAff	ACTIVATOR	INHIBITOR	K_ACTIVATORnodex	nu_ACTIVATORnodex	K_INHIBITORnodex	nu_INHIBITORnodex</blockquote>
&endEnhancerRegion</blockquote>
&endnodex</font></code>

*/
public class TxnSiteActInhibit3Aff extends Affector	{	
	/** The level of activator at which transcription proceeds half-maximally. */
	int		kParam, 
	/** The "cooperativity" exponent for activation. */
			nuParam,
	/** The level of inhibitor at which transcription is cut in half. */
		kInhibitParam,
	/** The "cooperativity" exponent for inhibition. */
		nuInhibitParam;

	static final String		desc = "Activated transcription - use this when combining several activators and inhibitor inside meta-affectors";
	static final String	[]	nodeDescriptions = {"Activator", "Inhibitor"};
	static final String	[]	paramDescriptions = {"Kappa_act: half-maximal level of activator",
										"nu_act: cooperativity of activation",
										"Kappa_inhibit: half-maximal level of inhibitor",
										"nu_inhibit: cooperativity of inhibition"};
	public TxnSiteActInhibit3Aff()	{}
	
	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];
		kInhibitParam = param_nums[2];
		nuInhibitParam = param_nums[3];
	}
	
	public float getValue(Node which_node)	{
		float	inhibition = Psi(Nodes[1].getIntegrationValue(), params[kInhibitParam], params[nuInhibitParam]);
		return	Phi(Nodes[0].getIntegrationValue(), params[kParam], params[nuParam]) * inhibition;
	}
}