package affectors;

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

/**	This is one half of a dimerization where the ligand and receptor can
bind within the same membrane as well as across different faces.  All Nodes, including
the dimer, must be membrane-bound. Use the A version of
this affector for the undimerized species.  Use the B version for the dimer.
The node_scale (max) for each of the singleton proteins is the scaling
factor for the >other< singleton.

<p> <b>Formula</b>
<br>dSINGLE_NODE1/dt = - r * max * SINGLE_NODE1 * SINGLE_NODE2

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Membrane Node [SINGLE_NODE1]</td><td> One undimerized Node </td></tr>
<tr><td width="150">Cytoplasmic Node [SINGLE_NODE2]</td><td> The other undimerized Node</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 >other< undimerized Node.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&SINGLE_NODE
<blockquote>    &DimerizeAllMembrane_AAff  SINGLE_NODE1  SINGLE_NODE2	r_DIMER	max
</blockquote>
&endSINGLE_NODE</code></font>
*/
public class DimerizeAllMembrane_AAff 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 nodes; version A for monomers";
	static final String	[]	nodeDescriptions = {"Target node", "Other node"};
	static final String	[]	paramDescriptions = {"Second-order reaction rate constant",
												"Scale factor (max value) for other node"};
	static final int	[]	whichSides = {-1, -1, 1};
	
	public DimerizeAllMembrane_AAff()	{}

	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];
	}
	
	
	/** Overridden because this affector uses the same node in two places. */
	public void fixNodes(Cell cell, String [] node_names) throws Exception
	{
		String [] new_node_names = new String[3];
		new_node_names[0] = node_names[0];
		new_node_names[1] = new_node_names[2] = node_names[1];
		sides = new int[3];
		sides[0] = sides[1] = -1;
		sides[2] = side;
		super.fixNodes(cell, new_node_names);
	}
		
	public float getValue(Node which_node) {
		return -Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[0].getIntegrationValue(side)
					* (Nodes[1].getIntegrationValue(side) + Nodes[2].getIntegrationValue(otherSide));
	}
	
	public float getNCValue(Node which_node)  {
		return -Globals.characteristicTime * params[kParam] * params[nodeScaleParam]
					* (Nodes[1].getIntegrationValue(side) + Nodes[2].getIntegrationValue(otherSide));
	}
}