package affectors;

import main.Globals;
import main.Node;

/** This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic
protein, leading to a cytoplasmic complex.  Use this affector in the dimerized species.  Use
the A and B versions in the undimerized ones.  Be careful to put the membrane and cytoplasmic
species in the right order in the initializer.  The node_scale you use for the dimer should
be the scale for the undimerized protein least similar to the dimer (i.e. for ligand/receptor
binding, you might use ligand0). 

<p> <b>Formula</b>
<br>dDIMER/dt = r * max * MEMBRANE_NODE * CYTO_NODE

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Membrane Node [MEMBRANE_NODE]</td><td> The undimerized Node that is on the membrane </td></tr>
<tr><td width="150">Cytoplasmic Node [CYTO_NODE]</td><td> The undimerized Node that is in the cytoplasm </td></tr>
<tr><td>Dimerization rate [r_DIMER]</td><td> The rate of the dimerization reaction.</td></tr>
<tr><td>Maximum Cyto [max]</td><td> The maximum relative concentration of the undimerized Node less similar to the dimer.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&DIMER
<blockquote>    &DimerizeMemCyto_CAff  MEMBRANE_NODE  CYTO_NODE	r_DIMER	max
</blockquote>
&endDIMER</code></font>
*/

public class DimerizeMemCyto_CAff extends Affector {
	/** The rate of the dimerization reaction. */
	int			kParam;
	/** The scaling factor of the other undimerized node in this reaction (i.e. max for second input node). */
	int			nodeScaleParam;
	
	static final String		desc = "Dimerize membrane-bound & cytoplasmic node; version C for dimer";
	static final String	[]	nodeDescriptions = {"Membrane-bound node", "Cytoplasmic node"};
	static final String	[]	paramDescriptions = {"Second-order reaction rate constant",
										"Scale factor (max value) for least-similar node"};
	static final int	[]	whichSides = {-1, -1};
	
	public DimerizeMemCyto_CAff()	{}
	
	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, nodeDescriptions, paramDescriptions);
		setSided(true, whichSides);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.FF;
		this.Type[TERMTYPE] = Affector.CONVERSION;
	}
	
	public void setParameterNumbers(int [] param_nums)
	{
		kParam = param_nums[0];
		nodeScaleParam = param_nums[1];
	}
	
	public float getValue(Node which_node) {
		return Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[0].getIntegrationValue() * Nodes[1].getIntegrationValue();
	}
}