package affectors;

import main.Globals;
import main.Node;



/** This is one third of a heterodimerization between a membrane bound and a cytoplasmic
protein, leading to a cytoplasmic complex.  Use this affector in the undimerized,
cytoplasmic species.  Use the A version in the membrane bound undimerized species and the
C version in the dimer.  Be careful to put the membrane and cytoplasmic species in the
right order in the initializer.  The node_scale for each of the singleton proteins is the
scaling factor for the >other< singleton (i.e. in the membrane node, give cytoNode0 as
node_scale and vice-versa). 

<p> <b>Formula</b>
<br>dCYTO_NODE/dt = - r * max_MEMBRANE_NODE * 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_MEMBRANE]</td><td> The maximum relative concentration of the membrane-bound Node.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&CYTO_NODE
<blockquote>    &DimerizeMemCyto_BAff  MEMBRANE_NODE  CYTO_NODE	r_DIMER	max_MEMBRANE
</blockquote>
&endCYTO_NODE</code></font>
*/

public class DimerizeMemCyto_BAff 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 membrane-bound node). */
	int			nodeScaleParam;
	
	static final String		desc = "Dimerize membrane-bound & cytoplasmic node; version B for cytoplasmic node";
	static final String	[]	nodeDescriptions = {"Membrane-bound node", "Cytoplasmic node"};
	static final String	[]	paramDescriptions = {"Second-order rate constant",
										"Scale factor (max value) for most-similar node"};
	static final int	[]	whichSides = {-1, -1};
	
	public DimerizeMemCyto_BAff()	{}
	
	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, nodeDescriptions, paramDescriptions);
		setSided(true, whichSides);
		setContainsTarget(true);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.GG;
		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();
	}
	
	public float getNCValue(Node which_node)  {
		return -Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[0].getIntegrationValue();
	}
}