package affectors;

import main.Node;
import main.Globals;

/** Txn3a takes two activators which synergize such that only in the presence of both can the 
target achieve full activity.  Parameters include as usual the half-life of the target and the
K's and nu's for each regulator, but also a "leak" parameter delta which enables one to specify
that one of the two activators can reach some fraction (equal to delta) in the absence of the
other (which behaves as a non-essential cofactor).  Delta should range from 0 (no leak in the 
absence of cofactor) to at most 1.0 (cofactor has no effect).  All inputs may be either 
cytoplasmic or membrane-bound as long as they reside in the same cell as the target.

<p> <b>Formula</b>
<br>ACTIVATION1 = ACTIVATOR1^nu_ACT1 / (K_ACT1^nu_ACT1 + ACTIVATOR1^nu_ACT1)
<br>ACTIVATION2 = ACTIVATOR2^nu_ACT2 / (K_ACT2^nu_ACT2 + ACTIVATOR2^nu_ACT2)
<br>dnodex/dt = (1 / H_nodex) * ACTIVATION1 * (delta + (1 - delta) * ACTIVATION2)
<p> <b>Parameters</b>

<table width="500" border="1">
<tr><td width="150">Activator1 [ACTIVATOR1]</td><td> The first transcriptional activator Node</td></tr>
<tr><td>Activator2 [ACTIVATOR2]</td><td> The second transcriptional activator Node, the "cofactor"</td></tr>
<tr><td>mRNA Half-life [H_nodex]</td><td> The half life of the product mRNA</td></tr>
<tr><td>Half-max activation level for first activator [K_ACTIVATOR1nodex]</td><td> The half-maximal concentration of the first activator</td></tr>
<tr><td>Activator 1 cooperativity [nu_ACTIVATOR1nodex]</td><td> The non-linearity for the first activator.  The higher the value, the sharper the curves in the S-shaped activation function</td></tr>
<tr><td>Half-max activation level for second activator [K_ACTIVATOR2nodex]</td><td> The half-maximal concentration of the cofactor</td></tr>
<tr><td>Activator 2 cooperativity [nu_ACTIVATOR2nodex]</td><td> The non-linearity for the second activator. The higher the value, the sharper the curves in the S-shaped activation function</td></tr>
<tr><td>Leak fraction [delta_ACTIVATOR1nodex]</td><td> The fraction of activation achievable in the absence of the cofactor</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>	&Txn3aAff ACTIVATOR1 ACTIVATOR2 H_nodex K_ACTIVATOR1nodex nu_ACTIVATOR1nodex K_ACTIVATOR2nodex nu_ACTIVATOR2nodex delta_ACTIVATOR1nodex</blockquote>
&endnodex</font></code>

*/
public class Txn3aAff extends Affector	{
	/** The half-life of the transcript. */
	int		halfLifeParam;
	/** The level of activator 1 at which transcription proceeds half-maximally. */
	int		kA1Param;
	/** The "cooperativity" exponent for activator 1. */
	int		nuA1Param;
	/** The level of activator 2 at which transcription proceeds half-maximally. */
	int		kA2Param;
	/** The "cooperativity" exponent for activator 2. */
	int		nuA2Param;
	/** The leak fraction. */
	int		deltaParam;
	
	static final String		desc = "Transcription dependent on two synergizing activators, one able to achieve a fractional output in the absence of the second";
	static final String	[]	nodeDescriptions = {"Activator 1", "Activator 2"};
	static final String	[]	paramDescriptions = {"Half-life of transcript produced",
										"Kappa activator 1: half-maximal level of activator 1",
										"nu1: cooperativity of activator 1",
										"Kappa activator 2: half-maximal level of activator 2",
										"nu2: cooperativity of activator 2",
										"delta: leak fraction"};
	
	public Txn3aAff()	{}
	
	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)
	{
		halfLifeParam = param_nums[0];
		kA1Param = param_nums[1];
		nuA1Param = param_nums[2];
		kA2Param = param_nums[3];
		nuA2Param = param_nums[4];
		deltaParam = param_nums[5];
	}

	public float getValue(Node which_node)	{
		
		float phi_A1=0, phi_A2=0;
		
		phi_A1 = Phi(Nodes[0].getIntegrationValue(), params[kA1Param], params[nuA1Param]);
		phi_A2 = Phi(Nodes[1].getIntegrationValue(), params[kA2Param], params[nuA2Param]);
		return ((Globals.characteristicTime / params[halfLifeParam]) * phi_A1 * (params[deltaParam] + ((1 - params[deltaParam]) * phi_A2)));
	}
	
}