main.cpp

/***************************************************************************
© Champak Beeravolu Reddy 2015-now

champak.br@gmail.com

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software.  You can  use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".

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modify and redistribute granted by the license, users are provided only
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with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
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***************************************************************************/

/*
 * main.cpp
 *
 *  Created on: 3 Jul 2015
 *      Author: champost
 */


#include <string>
#include <fstream>
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <cmath>
#include <cstdio>
#include <map>
#include <vector>
#include <algorithm>
#include <numeric>

#include "MersenneTwister.h"
#include "main.h"
#include "utils.h"

using namespace std;

//************ EXTERN **************
int brClass, mutClass, foldBrClass, allBrClasses, sampledPopsSize;
//**********************************

MTRand rMT;
map<vector<int>, int> intVec2BrConfig;
vector<int> sampledPops, allPops;
map<vector<int>, int> finalTableMap;

int ms_argc;
char **ms_argv;
int ntrees;


double ran1() { return(rMT()); }

void setMutConfigCount(int *singleConfig) {
        vector<int> singleConfigVec(singleConfig, singleConfig+brClass);
        ++finalTableMap[singleConfigVec];
}


string getMutConfigStr(vector<int> configVec) {
	int size = configVec.size();
	stringstream stst;
	stst << "(";
	for (int j = 0; j < size-1; j++)
		stst << configVec[j] << ",";
	stst << configVec[size-1] << ")";

	return stst.str();
}


int getPopSampleStatus(int pop) { return allPops[pop]; }

int getBrConfigNum(int *brConfVec) {
	vector<int> vec(brConfVec, brConfVec+sampledPops.size());
	return intVec2BrConfig[vec];
}


//	conversion from decimal to base-(maxPopSize+1)
void evalBranchConfigs() {
	int quo, rem, maxPopSize, totPopSum, count = 0, sumConfig;
	bool skipConfig;
	maxPopSize = totPopSum = sampledPops[0];

	for (size_t i = 1; i < sampledPops.size(); i++) {
		totPopSum += sampledPops[i];
		if (sampledPops[i] > maxPopSize)
			maxPopSize = sampledPops[i];
	}
	++maxPopSize;

	for (unsigned long int i = 1; i <= (unsigned long int) pow(maxPopSize,sampledPops.size()); i++) {
		quo = i;
		rem = 0;
/*
		stringstream stst;
		stst << ")";
*/
		sumConfig = 0;
		skipConfig = false;
		vector<int> vec;

		for (size_t j = 0; j < sampledPops.size(); j++) {
			if (quo) {
				rem = quo % (maxPopSize);
				quo /= (maxPopSize);
				if (rem > sampledPops[sampledPops.size()-1-j]) {
					skipConfig = true;
					break;
				}
//				stst << rem;
				sumConfig += rem;
				vec.push_back(rem);
			}
			else {
//				stst << "0";
				vec.push_back(0);
			}

/*
			if (j < sampledPops.size() - 1)
				stst << ",";
*/
		}

		if (sumConfig == totPopSum)
			break;

		if (!skipConfig) {
/*
			stst << "(";
			string config = stst.str();
			reverse(config.begin(),config.end());
*/
			reverse(vec.begin(),vec.end());
			intVec2BrConfig[vec] = count;
			++count;
/*
			printf("%d\t%d\t%s\n", i, count, config.c_str());
			printf("%d\t%s\n", count, config.c_str());
*/
		}
	}
}


void readPopSizes() {
	string line, del;
	vector<string> tokens;
	ifstream ifs("popconfig.txt",ios::in);
	while (getline(ifs,line)) {
		del = " ";
		tokens.clear();
		Tokenize(line, tokens, del);
		for(unsigned int j=0;j<tokens.size();j++)
			TrimSpaces(tokens[j]);

		if ((tokens[0][0] != '#') && (line.size() > 0)) {
			for (size_t i = 0; i < tokens.size(); i++) {
				stringstream stst(tokens[i]);
				if (stst.str() != "u") {
					int tmp;
					stst >> tmp;
					sampledPops.push_back(tmp);
					allPops.push_back(1);
				}
				else
					allPops.push_back(0);
			}
			sampledPopsSize = sampledPops.size();
		}
	}
	ifs.close();
}


int main(int argc, char* argv[]) {

//	int nsam = atoi(argv[1]);
	int kmax = atoi(argv[argc-2]);
	char brFold = argv[argc-1][0];
	ntrees = atoi(argv[2]);

	readPopSizes();

	brClass = sampledPops[0]+1;
	for (size_t i = 1; i < sampledPops.size(); i++)
		brClass *= (sampledPops[i]+1);
	brClass -= 2;
	allBrClasses = brClass;
	foldBrClass = 0;

	//	fold the branch classes
	if (brFold == 'f') {
		if (brClass % 2)
			brClass = (brClass+1) / 2;
		else
			brClass = brClass / 2;
		foldBrClass = 1;
	}

	if (kmax == 0)
		mutClass = 0;
	else
		mutClass = kmax+2;

//	printf("Total number of (possible) configs: %.0f\n", pow(mutClass, brClass));
//	exit(-1);

	evalBranchConfigs();

	// calling ms
	ms_argc = argc - 2;
	ms_argv = argv;
	main_ms(ms_argc, ms_argv);

//	double loglik = 0.0;
	for (map<vector<int>, int>::iterator it = finalTableMap.begin(); it != finalTableMap.end(); it++) {
		printf("%s : %d\n", getMutConfigStr(it->first).c_str(), it->second);
//		printf("%s : %.5e\n", getMutConfigStr(it->first).c_str(), (double) it->second/ntrees);
//		loglik += (log(it->second)-log(ntrees)) * it->second/ntrees;
	}
//	printf("LnL = %.6f\n", loglik);

	return 0;
}