package affectors;

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

/** Txn2b implements transcriptional activation under the control of one extracellular
activator expressed on neighboring cells and one cytoplasmic inhibitor, the latter of
which competetively inhibits the activator.  The inhibitor behaves as if it titrates
away the activator according to some dose-response curve; another way to look at it
is that the inhibitor raises the threshhold for activation.
<p> <b>Formula</b>
<br>EFFECTIVE_ACT = ACTIVATOR(neighbors) * ( 1 - INHIBITOR^nu_INHIB / (K_INHIBITOR^nu_INHIB + INHIBITOR^nu_INHIB))
<br>dnodex/dt = (1 / H_nodex) * EFFECTIVE_ACT^nu_ACT / (K_ACT^nu_ACT + EFFECTIVE_ACT^nu_ACT)
<p> <b>Parameters</b>

<table width="500" border="1">
<tr><td width="150">Inhibitor [INHIBITOR]</td><td> The inhibitor Node</td></tr>
<tr><td>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>Activator 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>
<tr><td>Half-max inhibition level [K_INHIBITOR]</td><td> The concentration of inhibitor at which transcription proceeds at half the rate it would have otherwise</td></tr>
<tr><td>Inhibition Cooperativity [nu_INHIBITOR]</td><td> The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>   &Txn2bAff	INHIBITOR	ACTIVATOR	K_ACTIVATORnodex	nu_ACTIVATORnodex	H_nodex	K_INHIBITORnodex	nu_INHIBITORnodex</blockquote>
&endnodex</font></code>

<p> NOTE - you can accomplish this same function using the meta-enhancers, and those are a
more general framework for putting together transcription terms.
*/

public class Txn2bAff 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;
	/** The level of inhibitor at which half the activator has been neutralized. */
	int		kInhibitParam;
	/** The "cooperativity" exponent for inhibition. */
	int		rhoParam;
	
	static final String		desc = "Transcription dependent on an activator, squelched by an inhibitor";
	static final String	[]	nodeDescriptions = {"Inhibitor", "Activator"};
	static final String	[]	paramDescriptions = {"Kappa activator: half-maximal level of activator",
										"nu: cooperativity of activation",
										"Half-life of transcript produced",
										"Kappa inhibitor: half-maximal level of inhibitor",
										"rho: cooperativity of inhibition"};
	
	public Txn2bAff()	{}
	
	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];
		kInhibitParam = param_nums[3];
		rhoParam = param_nums[4];
	}

	public float getValue(Node which_node)	{
		
		float total_activator = 0;
		float modulation;
		
		// total_activator sums contributions from all six neighbors, thus integrating sided input into non-sided form
		for(int i = 1; i <= Globals.cellNumSides; i++)	{
			total_activator += Nodes[i].getIntegrationValue(getOtherSide(i-1));
		}
		modulation = Psi(Nodes[0].getIntegrationValue(0),params[kInhibitParam],params[rhoParam]);
		return ((Globals.characteristicTime / params[halfLifeParam]) *
				Phi(total_activator*modulation,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 + 1];
			int i;
			Nodes[0] = cell.getNode(node_names[0]);	// inhibitor is intracellular
			for(i = 1; i <= Globals.cellNumSides; i++)	{
				Nodes[i] = cell.getNeighborNode(i-1,node_names[1]);	// activator is extracellular
			}
			notFixed = false;
		}
	}

}