/*
 *
 *
 *    Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements.
 *    See the NOTICE file distributed with this work for additional information regarding copyright ownership.
 *    The ASF licenses this file to You under the Apache License, Version 2.0 (the "License"); you may not use
 *    this file except in compliance with the License.  You may obtain a copy of the License at
 *
 *            http://www.apache.org/licenses/LICENSE-2.0
 *
 *    Unless required by applicable law or agreed to in writing, software distributed under the License is
 *    distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *    See the License for the specific language governing permissions and limitations under the License.
 *
 *
 */

package eu.amidst.dynamic.examples.inference;

import eu.amidst.core.variables.Assignment;
import eu.amidst.core.variables.Variable;
import eu.amidst.dynamic.models.DynamicBayesianNetwork;
import eu.amidst.dynamic.utils.DynamicBayesianNetworkGenerator;
import eu.amidst.dynamic.variables.DynamicAssignment;
import eu.amidst.dynamic.variables.HashMapDynamicAssignment;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.stream.Collectors;

/**
 * This example shows how to use the Dynamic MAP Inference algorithm described in Deliverable 3.4 (Section 6).
 * Created by dario on 11/11/15.
 */
public class DynamicMAPInference {

    public static void main(String[] arguments) throws IOException, ClassNotFoundException {

        /*
         * LOADS THE DYNAMIC NETWORK AND PRINTS IT
         */
        DynamicBayesianNetworkGenerator.setNumberOfContinuousVars(3);
        DynamicBayesianNetworkGenerator.setNumberOfDiscreteVars(5);
        DynamicBayesianNetworkGenerator.setNumberOfStates(2);
        DynamicBayesianNetworkGenerator.setNumberOfLinks(5);

        DynamicBayesianNetwork dynamicBayesianNetwork = DynamicBayesianNetworkGenerator.generateDynamicNaiveBayes(new Random(0), 2, true);


        /*
         *  INITIALIZE THE DYNAMIC MAP OBJECT
         */
        int nTimeSteps = 6;
        eu.amidst.dynamic.inference.DynamicMAPInference dynMAP = new eu.amidst.dynamic.inference.DynamicMAPInference();
        dynMAP.setModel(dynamicBayesianNetwork);
        dynMAP.setNumberOfTimeSteps(nTimeSteps);

        Variable mapVariable = dynamicBayesianNetwork.getDynamicVariables().getVariableByName("ClassVar");
        dynMAP.setMAPvariable(mapVariable);


        /*
         * GENERATE AN EVIDENCE FOR T=0,...,nTimeSteps-1
         */
        List<Variable> varsDynamicModel = dynamicBayesianNetwork.getDynamicVariables().getListOfDynamicVariables();

        System.out.println("DYNAMIC VARIABLES:");
        varsDynamicModel.forEach(var -> System.out.println("Var ID " + var.getVarID() + ": " + var.getName()));
        System.out.println();
        int indexVarEvidence1 = 2;
        int indexVarEvidence2 = 3;
        int indexVarEvidence3 = 4;
        Variable varEvidence1 = varsDynamicModel.get(indexVarEvidence1);
        Variable varEvidence2 = varsDynamicModel.get(indexVarEvidence2);
        Variable varEvidence3 = varsDynamicModel.get(indexVarEvidence3);

        List<Variable> varsEvidence = new ArrayList<>(3);
        varsEvidence.add(0,varEvidence1);
        varsEvidence.add(1,varEvidence2);
        varsEvidence.add(2,varEvidence3);

        double varEvidenceValue;

        Random random = new Random(4634);

        List<DynamicAssignment> evidence = new ArrayList<>(nTimeSteps);

        for (int t = 0; t < nTimeSteps; t++) {
            HashMapDynamicAssignment dynAssignment = new HashMapDynamicAssignment(varsEvidence.size());

            for (int i = 0; i < varsEvidence.size(); i++) {

                dynAssignment.setSequenceID(12302253);
                dynAssignment.setTimeID(t);
                Variable varEvidence = varsEvidence.get(i);

                if (varEvidence.isMultinomial()) {
                    varEvidenceValue = random.nextInt(varEvidence1.getNumberOfStates());
                } else {
                    varEvidenceValue = -5 + 10 * random.nextDouble();
                }
                dynAssignment.setValue(varEvidence, varEvidenceValue);
            }
            evidence.add(dynAssignment);
        }
        System.out.println("EVIDENCE:");
        evidence.forEach(evid -> {
            System.out.println("Evidence at time " + evid.getTimeID());
            evid.getVariables().forEach(variable -> System.out.println(variable.getName() + ": " + Integer.toString((int) evid.getValue(variable))));
            System.out.println();
        });

        /*
         *  SET THE EVIDENCE AND MAKE INFERENCE
         */
        dynMAP.setEvidence(evidence);
        dynMAP.runInference(eu.amidst.dynamic.inference.DynamicMAPInference.SearchAlgorithm.IS);

        /*
         *  SHOW RESULTS
         */
        Assignment MAPestimate = dynMAP.getMAPestimate();
        double MAPestimateProbability = dynMAP.getMAPestimateProbability();

        System.out.println("MAP sequence over " + mapVariable.getName() + ":");
        List<Variable> MAPvarReplications = MAPestimate.getVariables().stream().sorted((var1,var2) -> (var1.getVarID()>var2.getVarID()? 1 : -1)).collect(Collectors.toList());

        StringBuilder sequence = new StringBuilder();
        MAPvarReplications.stream().forEachOrdered(var -> sequence.append(Integer.toString((int) MAPestimate.getValue(var)) + ", "));
        //System.out.println(MAPestimate.outputString(MAPvarReplications));
        System.out.println(sequence.toString());
        System.out.println("with probability prop. to: " + MAPestimateProbability);

    }
}

@@ -874,52 +874,8 @@
 e;%0A%0A
-import eu.amidst.core.variables.Assignment;%0A
 impo
@@ -1221,20 +1221,22 @@
 va.util.
-List
+Arrays
 ;%0Aimport
@@ -1246,22 +1246,20 @@
 va.util.
-Random
+List
 ;%0Aimport
@@ -1273,25 +1273,14 @@
 til.
-stream.Collectors
+Random
 ;%0A%0A/
@@ -4929,29 +4929,24 @@
     
-Assignment MAPestimat
+int%5B%5D MAPsequenc
 e = 
@@ -4958,23 +4958,23 @@
 P.getMAP
-estimat
+sequenc
 e();%0A   
@@ -5127,32 +5127,34 @@
 + %22:%22);%0A        
+//
 List%3CVariable%3E M
@@ -5300,25 +5300,85 @@
 .toList());%0A
-%0A
+        System.out.println(Arrays.toString(MAPsequence));%0A%0A//
         Stri
@@ -5415,24 +5415,26 @@
 gBuilder();%0A
+//
         MAPv
@@ -5551,24 +5551,26 @@
 ) + %22, %22));%0A
+//
         //Sy
@@ -5629,24 +5629,26 @@
 ications));%0A
+//
         Syst

Fix #44