package affectors;

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

/** Use for activation of transcription. Activates according to an S-shaped function
(Phi function) with a half maximal activation level K and a cooperativity nu. This is identical
to the Txn1Aff except that it 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>dnodex/dt = (ACTIVATOR/K)^nu / (1 + (ACTIVATOR/K)^nu)

<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>Half-max activation level [K_ACTIVATORnodex]</td><td> The concentration of activator at which transcription proceeds at half its maximal rate</td></tr>
<tr><td>Cooperativity [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>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>&EnhancerRegion	H_nodex
<blockquote>   &TxnSiteActivatorAff	ACTIVATOR	K_ACTIVATORnodex	nu_ACTIVATORnodex	</blockquote>
&endEnhancerRegion</blockquote>
&endnodex</font></code>

*/
public class TxnSiteActivatorAff extends Affector	{	
	/** The level of activator at which transcription proceeds half-maximally. */
	int		kParam, 
	/** The "cooperativity" exponent for activation. */
			nuParam;

	static final String		desc = "Activated transcription - use this when combining several activators and inhibitor inside meta-affectors";
	static final String	[]	nodeDescriptions = {"Activator"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal level of activator",
										"nu: cooperativity of activation"};
	public TxnSiteActivatorAff()	{}
	
	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 Phi(Nodes[0].getIntegrationValue(), params[kParam], params[nuParam]);
	}
}