ConditionalProbabilityIndex.java

package org.monarchinitiative.owlsim.compute.cpt;

import java.util.Map;

import org.monarchinitiative.owlsim.compute.cpt.impl.TwoStateConditionalProbabilityIndex;
import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;

/**
 * Index for storing the value of Pr(C=on | P1=P1s, P2=P2s, ..., Pn=Pns),
 * where C is a child class, P1..Pn are parent classes, and P1_s...P_ns are
 * the <i>states</i> of P1..Pn, where Pi_s &in; S.
 * 
 * There are two implementations:
 * 
 * <ul>
 *  <li>{@link TwoStateConditionalProbabilityIndex} S={on,unknown}
 *  <li>{@link ThreeStateConditionalProbabilityIndex} S={on,unknown,off}
 * </ul>
 * 
 * The interface is relatively low-level for speed. Entries are accessed using
 * the integer index of the child class C (clsIndex). For the parents' states, a second index is
 * created, psi, an integer 0<=i<|S|^n, where representing each possible state of each parent.
 * i.e. psi = 0 means P1=0,Pn=0,...,Pn=0.
 * 
 * 
 * @author cjm
 *
 */
public interface ConditionalProbabilityIndex {

	/**
	 * return Probability of C given P1=S1...Pn=Sn
	 * 
	 * @param clsIndex - integer encoding C
	 * @param parentsStatesIndex - integer encoding P1=S1...Pn=Sn
	 * @return Pr(C | P1=S1, P2=S2, ..., Pn=Sn)
	 */
	public Double getConditionalProbabilityChildIsOn(int clsIndex, int parentsStatesIndex);
	
	
	/**
	 * Called to set all CPs
	 * 
	 * @param kb
	 * @throws IncoherentStateException
	 */
	public void calculateConditionalProbabilities(BMKnowledgeBase kb) throws IncoherentStateException;

	/**
	 * Returns the number of possible different state combinations for the parents of C
	 * 
	 * @param <code>ci</code>childClassIndex
	 * @return |S|<sup>|pa(ci)|</sup>
	 */
	public int getNumberOfParentStates(int childClassIndex);
	
	
	/**
	 * Each possible combination of P1=P1_s,...,Pn=Pn_s is encoded as an integer;
	 * this method maps from the integer back to a map of parents to states
	 * 
	 * @param clsIndex
	 * @param parentsState is a number between 0 and |S|^n
	 * @return map between class indices and states
	 */
	public Map<Integer, Character> getParentsToStateMapping(int clsIndex, int parentsState);

	
}