states = ["S", "I", "R"];

rules = [[ "I", "R", 1 ], // spontaneous rule  I -> R with rate 1.0
				[ "R", "S", 0.7 ],  // spontaneous rule R -> S with rate 0.7
				[ [ "I","S","I" ],[ "I","I","I" ], 0.8 ]]; // contact rule I+S -> I+I with rate 0.8


simulation = []


graph_as_edgelist = [[ 0, 4 ], [ 0, 1 ], [ 1, 5 ], [ 1, 2 ], [ 2, 6 ], [ 2, 3 ], [ 3, 7 ], [ 4, 8 ], [ 4, 5 ], [ 5, 9 ], [ 5, 6 ], [ 6, 10 ], [ 6, 7 ], [ 7, 11 ], [ 8, 12 ], [ 8, 9 ], [ 9, 13 ], [ 9, 10 ], [ 10, 14 ], [ 10, 11 ], [ 11, 15 ], [ 12, 13 ], [ 13, 14 ], [ 14, 15 ]];

horizon = 20.0;   // wie lange wird simuliert
initial_distribution = [0.5, 0.5, 0.0]; // gleiche Reihenfolge wie states, musss zu rules passen und normalisiert werden
timepoint_num = 101;

function get_next_state(current_labels){
  fastes_firing_time = 10000000.0;  //dummy
	firing_rule = null;
	firing_node = null;
	firing_edge = null;

	//if(current_labels == null)
	//iterate over nodes
	for(node in nodes){
		node = nodes[node];
		current_state = current_labels[node];
		for(rule in rules){
			rule = rules[rule];
			if(rule[0] instanceof Array){
				//is contact rule
				continue;
			}
			if(current_state == rule[0]){
				current_fireing_time = randomExponential(rule[2]);
				//addFiringTime(current_fireing_time);
				if(current_fireing_time < fastes_firing_time){
					fastes_firing_time = current_fireing_time;
					firing_rule = rule;
					firing_node = node;
					firing_edge = null;
				}
			}
		}
	}
	//iterate over edges
	for(edge in graph_as_edgelist){
		edge = graph_as_edgelist[edge];
		node1 = node2 = edge;
		current_state1 = current_labels[node1];
		current_state2 = current_labels[node2];
		for(rule in rules){
			rule = rules[rule];
			if(typeof rule[0] == typeof ""){
				//is spont. rule
				continue
			}
			if(current_state1 == rule[0][0] && current_state2 == rule[0][1] || current_state2 == rule[0][0] && current_state1 == rule[0][1]){
				current_fireing_time = randomExponential(rule[2]);
				if(current_fireing_time < fastes_firing_time){
					fastes_firing_time = current_fireing_time;
					firing_rule = rule;
					firing_node = null;
					firing_edge = edge;
				}
			}
		}
	}

	if(firing_rule == null){
		//no rule could fire
		return [null, fastes_firing_time]; //would happen anyway but still
	}
	//apply rule
	new_labels = Array.from(current_labels);

	if(firing_node != null){
		new_labels[firing_node] = firing_rule[1];
		return [new_labels, fastes_firing_time];
	}
	console.assert(firing_edge != null);
	change_node1 = firing_edge[0];
	change_node2 = firing_edge[1];
	//we have to check which node changes in which direction
	if(new_labels[change_node1] == firing_rule[0][0] && new_labels[change_node2] == firing_rule[0][1]){
		new_labels[change_node1] = firing_rule[1][0];
		new_labels[change_node2] = firing_rule[1][1];
	}else{
		new_labels[change_node1] = firing_rule[1][1];
		new_labels[change_node2] = firing_rule[1][0];
	}

	return [new_labels, fastes_firing_time];
}


function count_states(current_labels){
	counter = [states.length];
	simulation.push(current_labels);
	for(label in current_labels){
		label = current_labels[label];
		index = states[ label ];
		counter[index] += 1;
	}
}

function generateNodes(edgelist){
	allNodes = [];
	for(e in edgelist){
		e = edgelist[e];
		allNodes.push(e[0]);
		allNodes.push(e[1]);
	}
	//sort
	allNodes = allNodes.sort((a, b) => (a > b));
	//remove duplicates
	finalArray = [];
	var last = -1;
	for(var i = 0; i < allNodes.length; i ++){
		if(last == allNodes[i]){
			continue;
		}
		else{
			finalArray.push(allNodes[i])
			last = allNodes[i];
		}
	}
	return finalArray;
}

nodes = generateNodes(graph_as_edgelist);

//setup
timepoints_samples = linspace(0, horizon, timepoint_num);
timepoints_samples_static = linspace(0, horizon, timepoint_num);
current_labels = randomChoice(states, nodes.length, initial_distribution);
global_clock = 0;
labels = [];
timepoints = [];
state_counts = [];

simulate(rules, states, initial_distribution);
function simulate(newRules, newStates, newDistr){
	rules = newRules;
	states = newStates;
	initial_distribution = newDistr;
	while(timepoints_samples.length > 0){
		[new_labels, time_passed] = get_next_state(current_labels);
		global_clock += time_passed;
		while(timepoints_samples.length > 0 && global_clock > timepoints_samples[0]){
			labels.push(Array.from(current_labels));
			state_counts.push(count_states(current_labels));
			timepoints_samples = timepoints_samples.slice(1, timepoints_samples.length);
		}
		current_labels = new_labels;
	}
	console.log(simulation);
}

// np helper functions

function randomExponential(rate){
	if(rate == 0){ return 10000000 }
	return -Math.log(Math.random()) / rate;
}

function linspace(start, end, num){
	console.assert(start < end);
	console.assert(num > 0);
	distance = (end - start) / (num - 1);
	current = start;
	out = [];
	while(current <= end){
		out.push(Math.round(current * 100) / 100);
		current += distance;
	}
	return out;
}

function randomChoice(states, num, distr){
	out = [];
	let s = distr.reduce((a,e) => a + e);
	for(var i = 0; i < num; i++){
		let r = Math.random() * s;
		out.push(states.find((_,i) => (r -= distr[i]) < 0));
	}
	return out;
}

//times = [];
//function addFiringTime(time){
	//times.push(time);
//}
//
//function getAv(){
	//var sum = 0;
	//for(t in times){
		//t = times[t];
		//sum += t;
	//}
	//return sum / times.length;
//}
 //simulate();