package affectors;

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

/** The simplest regulated transcription affector. Transcription rate is a sigmoid function of 
activator concentration with transcription proceeding at half its maximum possible rate when
the activator concentration equals the half-max parameter, and with the rates on either side 
of this half-max dependent on how non-linear the sigmoid is.  The activator may be either
membrane-bound or intracellular, as long  as it is on the same cell as the target mRNA. 

<p> <b>Formula</b>
<br>dnodex/dt = (1 / H_nodex) * ACTIVATOR^nu / (K^nu + ACTIVATOR^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>
<tr><td>mRNA Half-life [H_nodex]</td><td> The half life of the product mRNA</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>   &Txn1Aff	ACTIVATOR	K_ACTIVATORnodex	nu ACTIVATORnodex	H_nodex</blockquote>
&endnodex</font></code>
*/
public class Txn1Aff extends Affector	{
	/** The level of activator at which transcription proceeds half-maximally. */
	int		kParam;
	/** The "cooperativity" exponent for activation. */
	int		nuParam;
	/** The half-life of the transcript. */
	int		halfLifeParam;

	static final String		desc = "Transcription dependent on an activator";
	static final String	[]	nodeDescriptions = {"Activator"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal level of activator",
										"nu: cooperativity of activation",
										"Half-life of transcript produced"};
	
	public Txn1Aff()	{}
	
	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];
		halfLifeParam = param_nums[2];
	}
	
	public float getValue(Node which_node)	{
		return ((Globals.characteristicTime / params[halfLifeParam]) *
				Phi(Nodes[0].getIntegrationValue(),params[kParam],params[nuParam]));
	}
}