package affectors;

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

/** A variant of <a href = Txn1Aff.html>Txn1Aff</a> that integrates an external influence from a neighboring cell
(e.g. a signalling protein) and activates transcription as a function of the total
activator presented on all cell faces. Use this if you want to skip the signal transduction
cascade between a ligand on neighboring cells and transcription. Everything else is
the same as <a href = Txn1Aff.html>Txn1Aff</a>.

<p> <b>Formula</b>
<br>dnodex/dt = (1 / H_nodex) * ACTIVATOR(neighbors)^nu / (K^nu + ACTIVATOR(neighbors)^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>   &Txn1ECAff	ACTIVATOR	K_ACTIVATORnodex	nu ACTIVATORnodex	H_nodex</blockquote>
&endnodex</font></code>
*/
public class Txn1ECAff 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 extrinsic 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 Txn1ECAff()	{	}
	
	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)	{
		
		float total_activator = 0;
		
		// total_activator sums contributions from all six neighbors, thus integrating sided input into non-sided form
		for(int i = 0; i< Globals.cellNumSides; i++)	{
			total_activator += Nodes[i].getIntegrationValue(getOtherSide(i));
		}
		return ((Globals.characteristicTime / params[halfLifeParam]) *
				Phi(total_activator,params[kParam],params[nuParam]));
	}
	
	// Affector::fixNodes over-ridden to fill Nodes[] with activator concentrations from all six neighbors; thus this non-sided affector uses a sided node
	public void fixNodes(Cell cell, String [] node_names) throws Exception	{
		if(notFixed)	{
			Nodes = new Node[Globals.cellNumSides];
			for(int i = 0; i < Globals.cellNumSides; i++)	{
				Nodes[i] = cell.getNeighborNode(i,node_names[0]);
			}
			notFixed = false;
		}
	}

}