Monoobjective resolution

 # Prerequisites
 *.d
 
+# LaTeX temporary files
+doc/*.toc
+doc/*.bbl
+doc/*.gz
+
 # Compiled Object files
 *.slo
 *.lo

+# Please set the following variables to the correct paths for JAR3D:
+jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar"
+ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib"
+HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib"
\ No newline at end of file

-# ------------------------------------------------
-# Generic Makefile
-# ------------------------------------------------
+ICONCERT=/opt/ibm/ILOG/CPLEX_Studio_Community128/concert/include
+ICPLEX=/opt/ibm/ILOG/CPLEX_Studio_Community128/cplex/include
+LCONCERT=/opt/ibm/ILOG/CPLEX_Studio_Community128/concert/lib/x86-64_linux/static_pic/
+LCPLEX=/opt/ibm/ILOG/CPLEX_Studio_Community128/cplex/lib/x86-64_linux/static_pic/
 
 # project name (generate executable with this name)
-TARGET   = motifscan
+TARGET   = biominserter
 
 CC	   = g++
 # compiling flags here
-CFLAGS   = -I. -O3
-CXXFLAGS = -std=c++17 -Wall -Wpedantic -Wextra
+CFLAGS   = -Icppsrc/ -I$(ICONCERT) -I$(ICPLEX) -O3
+CXXFLAGS = -std=c++17 -Wall -Wpedantic -Wextra -Wno-ignored-attributes
 
 LINKER   = g++
 # linking flags here
-LDFLAGS   = -lboost_system -lboost_filesystem -lboost_program_options
+LDFLAGS   = -lconcert -lilocplex -lcplex -lm -lpthread -ldl -lboost_system -lboost_filesystem -lboost_program_options -L$(LCONCERT) -L$(LCPLEX)
 
 # change these to proper directories where each file should be
-SRCDIR   = src
+SRCDIR   = cppsrc
 OBJDIR   = obj
 BINDIR   = bin
 

-# RNA_Motifs_Inserter
-A C++ software interface to RNA motif databases, and algorithms to include known motifs in raw sequences.
+This is a bi-objective integer programming algorithm.
+It predicts the secondary structure of a RNA sequence with pieces of 3D information (non-canonical contacts) at some places, 
+by identifying zones that can fold like known motifs.
+
+1/ How it works
+===================================
+INPUT:
+- An RNA sequence (tested with sequences ~100 bases)
+
+THEN
+- Identifies possible 2D folds with RNAsubopt.
+- Knowing possible 2D folds, locate every possibly unpaired loop (hairpin loop, internal loop, multiple junction...)
+- align each unpaired loop to the catalogue of models of known RNA motifs (The 3D Motif Atlas of the BGSU RNA group)
+- retrieve a list of potential motif-insertion-sites in the RNA sequence. Use them to define the constraints for the IP problem.
+- Solve a bi-objective IP problem: 
+    * Maximize the expected accuracy of the secondary structure,
+    * Maximize the number and size of motifs inserted in the structure.
+
+OUTPUT:
+- A set of secondary structures from the pareto front,
+- The list of known motif inserted in the corresponding structures (and the non-canonical contacts)
+- (Optionally, lower score structures from k-Pareto sets.)
+
+2/ Installation
+==================================
+- Download and install RNAsubopt from the ViennaRNA package (https://www.tbi.univie.ac.at/RNA/)
+- Download and install IBM ILOG Cplex optimization studio (https://www.ibm.com/analytics/cplex-optimizer), free academic account required
+- Download and install Java runtime (Tested with Java 10)
+- Download and install the latest JAR3D executable "jar3d_releasedate.jar" and motif models in this folder (http://rna.bgsu.edu/data/jar3d/models/)
+  Note that for HL and ILs, only the latest version is required (not all the versions provided in the folders).
+- Download and install a C++ compiler and building dependencies and utilities (g++ or clang, automake, libboost)

+#include "MOIP.h"
+#include "SecondaryStructure.h"
+#include "rna.h"
+#include <algorithm>
+#include <boost/format.hpp>
+#include <cfloat>
+#include <cmath>
+#include <cstdlib>
+#include <iostream>
+#include <limits>
+#include <stdexcept>
+#include <utility>
+#include <vector>
+
+using std::cerr, std::cout, std::endl;
+using std::make_pair;
+using std::vector;
+
+uint MOIP::ncores = 0;
+
+MOIP::MOIP(const RNA& rna, const vector<Motif>& insertionSites)
+: rna_(rna), insertion_sites_(insertionSites), beta_(1.0), theta_{1.0 / (2.0 + 1.0)}
+{
+    basepair_dv_  = IloNumVarArray(env_);
+    insertion_dv_ = IloNumVarArray(env_);
+
+    // Add the y^u_v decision variables
+    uint u, v, c = 0;
+    index_of_yuv_ = vector<vector<size_t>>(rna_.get_RNA_length() - 6, vector<size_t>(0));
+    for (u = 0; u < rna_.get_RNA_length() - 6; u++) {
+        for (v = u + 4; v < rna_.get_RNA_length(); v++)    // A basepair is possible iff v > u+3
+        {
+            index_of_yuv_[u].push_back(c);
+            c++;
+            char name[15];
+            sprintf(name, "y%d,%d", u, v);
+            basepair_dv_.add(IloNumVar(env_, 0, 1, IloNumVar::Bool, name));    // A boolean whether u and v are paired
+        }
+    }
+    // Add the Cx,i,p decision variables
+    index_of_first_components.reserve(insertionSites.size());
+    index_of_Cxip_ = vector<vector<size_t>>(0);
+    index_of_Cxip_.reserve(insertionSites.size());
+    size_t i = 0;
+    for (const Motif m : insertionSites) {
+        index_of_first_components.push_back(i);
+        index_of_Cxip_.push_back(vector<size_t>(0));
+        for (const Component c : m.comp) {
+            index_of_Cxip_.back().push_back(i);
+            if (c.k > 0) i++;
+            char name[20];
+            sprintf(
+            name,
+            "C%d,%d-%d",
+            static_cast<int>(index_of_Cxip_.size() - 1),
+            static_cast<int>(index_of_Cxip_.back().size() - 1),
+            c.pos.first);
+            insertion_dv_.add(IloNumVar(env_, 0, 1, IloNumVar::Bool, name));    // A boolean whether component i of motif x is inserted at position p
+        }
+    }
+    cout << i + c << " decision variables are used !" << endl;
+}
+
+
+MOIP::~MOIP() { env_.end(); }
+
+
+bool MOIP::is_undominated_yet(const SecondaryStructure& s)
+{
+    for (uint i = 0; i < pareto_.size(); i++) {
+        if (pareto_[i] > s) return false;
+    }
+    return true;
+}
+
+void MOIP::solve_objective(int o, double min, double max)
+{
+    IloModel model_ = IloModel(env_);
+    cout << "Solving objective function " << o << "..." << endl;
+    add_problem_constraints(model_);
+    switch (o) {
+    case 1: {
+        // Add the motif objective function
+        IloExpr obj1 = IloExpr(env_);
+        for (uint i = 0; i < insertion_sites_.size(); i++) {
+            IloNum n_compo_squared = IloNum(insertion_sites_[i].comp.size() * insertion_sites_[i].comp.size());
+            obj1 += n_compo_squared * insertion_dv_[index_of_first_components[i]];
+        }
+        model_.add(IloMinimize(env_, obj1));
+    } break;
+    case 2: {
+        // Add the likelihood objective function
+    }
+    }
+    IloCplex cplex_ = IloCplex(model_);
+    if (!cplex_.solve()) {
+        env_.error() << "\t>Failed to optimize LP." << endl;
+        throw(-1);
+    }
+    IloNumArray basepair_values(env_);
+    IloNumArray insertion_values(env_);
+    env_.out() << endl << "Solution status = " << cplex_.getStatus() << endl;
+    env_.out() << endl << "Objective value = " << cplex_.getObjValue() << endl;
+    cplex_.getValues(basepair_values, basepair_dv_);
+    env_.out() << endl << "Basepair Values = " << basepair_values << endl;
+    cplex_.getValues(insertion_values, basepair_dv_);
+    env_.out() << endl << "Insertion Values = " << insertion_values << endl;
+
+    // TODO : retrieve the secondary structure !!
+}
+
+void MOIP::add_problem_constraints(const IloModel& model_)
+{
+    // ensure there only is 0 or 1 pairing by nucleotide:
+    cout << "\t>ensuring there are 0 or 1 pairing by nucleotide..." << endl;
+    uint u, v;
+    uint n = rna_.get_RNA_length();
+    for (u = 0; u < n - 6; u++) {
+        IloExpr c1(env_);
+        for (v = 0; v < u; v++)
+            if (allowed_basepair(v, u)) c1 += y(v, u);
+        for (v = u + 4; v < n; v++)
+            if (allowed_basepair(u, v)) c1 += y(u, v);
+        model_.add(c1 <= 1);
+        // cout << "\t>It worked for base " << u << " : " << (c1 <= 1) << endl;
+    }
+    // forbid lonely basepairs
+    cout << "\t>forbidding lonely basepairs..." << endl;
+    for (u = 0; u < n - 6; u++) {
+        IloExpr c2(env_);    // for the case where s[u] is paired to s[v], v>u
+        c2 += 1;
+        for (v = u; v < n; v++)
+            if (allowed_basepair(u - 1, v)) c2 += y(u - 1, v);
+        for (v = u + 1; v < n; v++)
+            if (allowed_basepair(u, v)) c2 -= y(u, v);
+        for (v = u + 2; v < n; v++)
+            if (allowed_basepair(u + 1, v)) c2 += y(u + 1, v);
+        model_.add(c2 >= 1);
+        // cout << "\t>It worked for base " << u << " : " << (c2 >= 1) << endl;
+    }
+    for (v = 5; v < n; v++) {
+        IloExpr c2p(env_);    // for the case where s[u] is paired to s[v], v<u
+        c2p += 1;
+        for (u = 1; u <= v - 2; u++)
+            if (allowed_basepair(u, v - 1)) c2p += y(u, v - 1);
+        for (u = 1; u <= v - 1; u++)
+            if (allowed_basepair(u, v)) c2p -= y(u, v);
+        for (u = 1; u <= v; u++)
+            if (allowed_basepair(u, v + 1)) c2p += y(u, v + 1);
+        model_.add(c2p >= 1);
+        // cout << "\t>It worked for base " << u << " : " << (c2p >= 1) << endl;
+    }
+    // Forbid pairings inside every motif component if included
+    cout << "\t>forbidding basepairs inside included motif's components..." << endl;
+    for (size_t i = 0; i < insertion_sites_.size(); i++) {
+        Motif& x = insertion_sites_[i];
+        for (size_t j = 0; j < x.comp.size(); j++) {
+            Component& c = x.comp[j];
+            IloExpr    c3(env_);
+            IloNum     kxi = IloNum(c.k);
+            c3 += kxi * C(i, j);
+            for (u = c.pos.first; u < c.pos.second; u++) {
+                for (v = 0; v < n; v++)
+                    if (allowed_basepair(u, v)) c3 += y(u, v);
+            }
+            model_.add(c3 <= kxi);
+        }
+    }
+    // To be continued ...
+}
+
+void MOIP::extend_pareto(double lambdaMin, double lambdaMax)
+{
+    if (lambdaMin >= lambdaMax) {
+        cerr << "lambdaMax < lambdaMin, something's wrong !" << endl;
+        exit(EXIT_FAILURE);
+    }
+
+    // for any SecondaryStructure in pareto_ such that the value of the second
+    // objective is between lambdaMin and lambdaMax
+    // a DIFF() constraint and a mirror constraint is added
+    for (uint i = 0; i < pareto_.size(); i++) {
+        // DIFF()
+        if (
+        (abs(pareto_[i].get_objective_score(2) - lambdaMin) < PRECISION or pareto_[i].get_objective_score(2) > lambdaMin) and
+        (abs(pareto_[i].get_objective_score(2) - lambdaMax) < PRECISION or pareto_[i].get_objective_score(2) < lambdaMax)) {
+            // ip.add_bj_ct(pareto_[i]);
+        }
+        // mirror
+        // if (
+        // (abs(pareto_[i].get_obj2M_() - lambdaMin) < PRECISION or pareto_[i].get_obj2M_() > lambdaMin) and
+        // (abs(pareto_[i].get_obj2M_() - lambdaMax) < PRECISION or pareto_[i].get_obj2M_() < lambdaMax)) {
+        //     ip.add_bj_ct_M(pareto_[i]);
+        // }
+    }
+
+    // SecondaryStructure s = solve_objective(1, lambdaMin, lambdaMax);
+
+    // if (is_undominated_yet(s)) {
+    //     // adding the SecondaryStructure s to the set pareto_
+    //     add_solution(s);
+    //     // run localPareto above the SecondaryStructure s
+    //     extend_pareto(s.get_objective_score(2), lambdaMax);
+    // }
+}
+
+size_t MOIP::get_yuv_index(size_t u, size_t v) const
+{
+    size_t a, b;
+    a = (u < v) ? u : v;
+    b = (u > v) ? u : v;
+    return index_of_yuv_[a][b - 4 - a];
+}
+
+size_t MOIP::get_Cpxi_index(size_t x_i, size_t i_on_j) const { return index_of_Cxip_[x_i][i_on_j]; }
+
+
+bool MOIP::allowed_basepair(size_t u, size_t v) const
+{
+    size_t a, b;
+    a = (v > u) ? u : v;
+    b = (v > u) ? v : u;
+    if (b - a < 4) return false;
+    if (a >= rna_.get_RNA_length() - 6) return false;
+    if (b >= rna_.get_RNA_length()) return false;
+    return true;
+}
\ No newline at end of file

+#ifndef MOIP_H_
+#define MOIP_H_
+
+#define IL_STD
+
+#include "SecondaryStructure.h"
+#include "rna.h"
+#include <ilcplex/ilocplex.h>
+
+using std::vector;
+
+const double PRECISION = 0.0001;
+
+
+class MOIP
+{
+  public:
+    static uint ncores;
+    typedef enum { MIN, MAX } DirType;
+    typedef enum { FR, LO, UP, DB, FX } BoundType;
+    MOIP(const RNA& rna, const vector<Motif>& motifSites);
+    ~MOIP(void);
+    void                      solve_objective(int o, double min, double max);
+    uint                      get_n_solutions(void) const;
+    const SecondaryStructure& solution(uint i) const;
+    void                      extend_pareto(double lambdaMin, double lambdaMax);
+    bool                      allowed_basepair(size_t u, size_t v) const;
+    void                      add_solution(const SecondaryStructure& s);
+
+  private:
+    bool           is_undominated_yet(const SecondaryStructure& s);
+    void           add_problem_constraints(const IloModel& model_);
+    size_t         get_yuv_index(size_t u, size_t v) const;
+    size_t         get_Cpxi_index(size_t x_i, size_t i_on_j) const;
+    IloNumExprArg& y(size_t u, size_t v);    // Direct reference to y^u_v in basepair_dv_
+    IloNumExprArg& C(size_t x, size_t i);    // Direct reference to C_p^xi in insertion_dv_
+
+
+    RNA                        rna_;                // RNA object
+    vector<Motif>              insertion_sites_;    // Potential Motif insertion sites
+    const float                beta_;               // beta parameter of the probability function
+    double                     lambdaMin_;          // minimum threshold value for the probability value
+    double                     lambdaMax_;          // maximum threshold value for the probability value
+    int                        vp_;                 // vp_ variable for penalization of the probability score
+    float                      theta_;              // theta parameter for the probability function
+    IloEnv                     env_;                // environment CPLEX object
+    IloNumVarArray             basepair_dv_;        // Decision variables
+    IloNumVarArray             insertion_dv_;       // Decision variables
+    vector<SecondaryStructure> pareto_;             // Vector of results
+    vector<vector<size_t>>     index_of_Cxip_;      // Stores the indexes of the Cxip in insertion_dv_
+    vector<vector<size_t>>     index_of_yuv_;    // Stores the indexes of the y^u_v in basepair_dv_ in a complex way. Use get_yuv_index(u,v) to retrieve.
+    vector<size_t>             index_of_first_components;    // Stores the indexes of Cx1p in insertion_dv_
+};
+
+inline void                      MOIP::add_solution(const SecondaryStructure& s) { pareto_.push_back(s); }
+inline uint                      MOIP::get_n_solutions(void) const { return pareto_.size(); }
+inline const SecondaryStructure& MOIP::solution(uint i) const { return pareto_[i]; }
+inline IloNumExprArg&            MOIP::y(size_t u, size_t v) { return basepair_dv_[get_yuv_index(u, v)]; }
+inline IloNumExprArg&            MOIP::C(size_t x, size_t i) { return insertion_dv_[get_Cpxi_index(x, i)]; }
+
+#endif    // MOIP_H_
\ No newline at end of file

+#include "SecondaryStructure.h"
+#include <boost/format.hpp>
+
+static const double PRECISION(0.0001);
+
+SecondaryStructure::SecondaryStructure(const vector<double>& scores, const vector<bool>& decision_variables, VII coord, int RNAlength)
+: objective_scores_(scores), dv_(decision_variables), coord_(coord), n_(RNAlength)
+{
+}
+
+string SecondaryStructure::to_DBN(void) const
+{
+    string res(n_, '.');
+    for (size_t i = 0; i < n_; i++) {
+        if (dv_[i]) {
+            res[coord_[i].first]  = '(';
+            res[coord_[i].second] = ')';
+        }
+    }
+    return res;
+}
+
+string SecondaryStructure::to_string(void) const
+{
+    return to_DBN() + "\t" + boost::str(boost::format("%.6f") % objective_scores_[0]) + "\t" +
+           boost::str(boost::format("%.6f") % objective_scores_[1]);
+}
+
+bool operator>(const SecondaryStructure& s1, const SecondaryStructure& s2)
+{
+    double s11 = s1.get_objective_score(0);
+    double s12 = s1.get_objective_score(1);
+    double s21 = s2.get_objective_score(0);
+    double s22 = s2.get_objective_score(1);
+
+    bool obj1 = false, obj2 = false, strict1 = false, strict2 = false;
+
+    if (s11 > s21) {
+        strict1 = true;
+        obj1    = true;
+    } else if (abs(s11 - s21) < PRECISION) {
+        obj1 = true;
+    }
+    if (s12 > s22) {
+        strict2 = true;
+        obj2    = true;
+    } else if (abs(s12 - s22) < PRECISION) {
+        obj2 = true;
+    }
+
+    if (obj1 && obj2 && (strict1 || strict2)) {
+        return true;
+    }
+
+    return false;
+}
+
+bool operator<(const SecondaryStructure& s1, const SecondaryStructure& s2)
+{
+    double s11 = s1.get_objective_score(0);
+    double s12 = s1.get_objective_score(1);
+    double s21 = s2.get_objective_score(0);
+    double s22 = s2.get_objective_score(1);
+
+    bool obj1 = false, obj2 = false, strict1 = false, strict2 = false;
+
+    if (s11 < s21) {
+        strict1 = true;
+        obj1    = true;
+    } else if (abs(s11 - s21) < PRECISION) {
+        obj1 = true;
+    }
+    if (s12 < s22) {
+        strict2 = true;
+        obj2    = true;
+    } else if (abs(s12 - s22) < PRECISION) {
+        obj2 = true;
+    }
+
+    if (obj1 && obj2 && (strict1 || strict2)) {
+        return true;
+    }
+    return false;
+}

+#ifndef __INC_IP_SOL__
+#define __INC_IP_SOL__
+
+#include "rna.h"
+#include <string>
+#include <vector>
+
+using std::string;
+using std::vector;
+
+typedef vector<int>                 VI;
+typedef vector<VI>                  VVI;
+typedef vector<std::pair<int, int>> VII;
+
+
+class SecondaryStructure
+{
+  public:
+    SecondaryStructure(void);
+    SecondaryStructure(const vector<double>& scores, const vector<bool>& decision_variables, VII coord, int RNAlength);
+
+    double              get_objective_score(int i) const;
+    const vector<bool>& get_decision_variables() const;
+    bool                get_decision_value(int i) const;
+    VII                 get_coord() const;
+    int                 get_RNA_length() const;
+
+    void   set_objective_score(int i, double s);
+    string to_DBN() const;
+    string to_string() const;
+
+  private:
+    vector<double> objective_scores_;    // values of the different objective functions for that SecondaryStructure
+    vector<bool>   dv_;                  // values of the decision variable of the integer program
+    vector<Motif>  motif_info_;    // information about known motives in this secondary structure and their positions
+    VII            coord_;         // coordinates of the dv_. dv_[i] == true <==> coord_[i][0] paired to coord_[i][1];
+    size_t         n_;             // length of the RNA
+};
+
+// return if this SecondaryStructure s1 dominates s2
+bool operator>(const SecondaryStructure& s1, const SecondaryStructure& s2);
+// return if this SecondaryStructure s2 dominates s1
+bool operator<(const SecondaryStructure& s1, const SecondaryStructure& s2);
+
+inline double              SecondaryStructure::get_objective_score(int i) const { return objective_scores_[i]; }
+inline const vector<bool>& SecondaryStructure::get_decision_variables() const { return dv_; }
+inline void                SecondaryStructure::set_objective_score(int i, double s) { objective_scores_[i - 1] = s; }
+inline VII                 SecondaryStructure::get_coord() const { return coord_; }
+inline int                 SecondaryStructure::get_RNA_length() const { return n_; }
+inline bool                SecondaryStructure::get_decision_value(int i) const { return dv_[i]; }
+
+#endif

+/***
+        Biominserter
+        Louis Becquey, starting from Audrey Legendre's code
+        nov 2018
+***/
+
+#include <algorithm>
+#include <boost/algorithm/string.hpp>
+#include <cstdlib>
+#include <iostream>
+#include <iterator>
+#include <string>
+#include <thread>
+#include <vector>
+
+#include "MOIP.h"
+#include "fa.h"
+#include "nupack.h"
+
+using namespace std;
+
+Motif parse_csv_line(string line)
+{
+    vector<string> tokens;
+    boost::split(tokens, line, boost::is_any_of(","));
+    Motif m;
+    m.atlas_id = tokens[0];
+    m.comp.push_back(Component(make_pair<int, int>(stoi(tokens[3]), stoi(tokens[4])), stoi(tokens[2])));
+    if (tokens[5] != "-")
+        m.comp.push_back(Component(make_pair<int, int>(stoi(tokens[5]), stoi(tokens[6])), stoi(tokens[2])));
+    m.reversed = (tokens[1] == "True");
+    return m;
+}
+
+int main(int argc, char* argv[])
+{
+    // float   time;
+    // clock_t t1, t2;
+    // t1 = clock();
+
+    MOIP::ncores = thread::hardware_concurrency() - 1;
+
+    if (argc != 3) {
+        cerr << argc << " arguments specified !" << endl;
+        cerr << "Please specify the following input files:" << endl;
+        cerr << "biominserter sequence.fasta insertion.sites.csv" << endl;
+        return EXIT_FAILURE;
+    }
+
+
+    const char* inputName = argv[1];
+    const char* csvname   = argv[2];
+    cout << "Reading input files..." << endl;
+    if (access(inputName, F_OK) == -1) {
+        cerr << inputName << " not found" << endl;
+        return EXIT_FAILURE;
+    }
+    if (access(csvname, F_OK) == -1) {
+        cerr << csvname << " not found" << endl;
+        return EXIT_FAILURE;
+    }
+
+    // load fasta file
+    list<Fasta> f;
+    Fasta::load(f, inputName);
+    list<Fasta>::iterator fa = f.begin();
+    cout << "loading " << fa->name() << "..." << endl;
+    RNA myRNA = RNA(fa->name(), fa->seq());
+    cout << "\t>" << inputName << " successfuly loaded" << endl;
+
+    // load CSV file
+    string   line;
+    ifstream motifs = ifstream(csvname);
+    getline(motifs, line);    // skip header
+    vector<Motif> posInsertionSites;
+    while (getline(motifs, line)) {
+        posInsertionSites.push_back(parse_csv_line(line));
+    }
+    cout << "\t>" << csvname << " successfuly loaded" << endl;
+
+    // creating the Multi-Objective problem:
+    MOIP myMOIP = MOIP(myRNA, posInsertionSites);    // using the constructor with arguments automatically defines the decision variables.
+
+    // finding the best SecondaryStructures for each objective
+    double max = myRNA.get_RNA_length();
+    try {
+        myMOIP.solve_objective(1, -max, max);
+    } catch (IloCplex::Exception& e) {
+        cerr << e << endl;
+    }
+    // SecondaryStructure bestSSO1 = myMOIP.solve_objective(1, -max, max);
+    // SecondaryStructure bestSSO2 = myMOIP.solve_objective(2, -max, max);
+    // double             bestObj2 = bestSSO2.get_objective_score(2);
+
+    // extend to the whole pareto set
+    // myMOIP.add_solution(bestSSO1);
+    // myMOIP.extend_pareto(bestObj2, max);
+
+    // print the pareto set
+    // cout << "Structure \t Free energy score \t Expected accuracy score" << endl;
+    // for (uint i = 0; i < myMOIP.get_n_solutions(); i++) {
+    //     cout << myMOIP.solution(i).to_string() << endl;
+    // }
+    // cout << endl;
+
+    return EXIT_SUCCESS;
+}

+/*
+ * $Id$
+ *
+ * Copyright (C) 2010 Kengo Sato
+ *
+ * doublehis file comes from IPknot.
+ *
+ */
+
+#ifndef __INC_DP_TABLE_H__
+#define __INC_DP_TABLE_H__
+
+class DPtable2
+{
+  public:
+    DPtable2() : V_(), N_(0) {}
+    void resize(int n)
+    {
+        N_ = n;
+        V_.resize(N_ * (N_ + 1) / 2 + (N_ + 1));
+    }
+    void          fill(const double& v) { std::fill(V_.begin(), V_.end(), v); }
+    double&       operator()(int i, int j) { return V_[index(i, j)]; }
+    const double& operator()(int i, int j) const { return V_[index(i, j)]; }
+
+  private:
+    int index(int i, int j) const
+    {
+        assert(j <= N_);
+        return j == i - 1 ? N_ * (N_ + 1) / 2 + i : i * N_ + j - i * (1 + i) / 2;
+    }
+    std::vector<double> V_;
+    int                 N_;
+};
+
+class DPtable4
+{
+  public:
+    DPtable4() : V_(), N_(0) {}
+    void resize(int n)
+    {
+        N_ = n;
+        V_.resize(N_ * (N_ - 1) * (N_ - 2) * (N_ - 3) / 2 / 3 / 4);
+    }
+    void          fill(const double& v) { std::fill(V_.begin(), V_.end(), v); }
+    double&       operator()(int i, int d, int e, int j) { return V_[index(i, d, e, j)]; }
+    const double& operator()(int i, int d, int e, int j) const { return V_[index(i, d, e, j)]; }
+
+  private:
+    int index(int h, int r, int m, int s) const
+    {
+        int n  = N_;
+        int h2 = h * h;
+        int h3 = h2 * h;
+        int h4 = h3 * h;
+        int m2 = m * m;
+        int n2 = n * n;
+        int n3 = n2 * n;
+        int r2 = r * r;
+        int r3 = r2 * r;
+        assert(h <= r);
+        assert(r <= m);
+        assert(m <= s);
+        assert(s <= N_);
+        return (h == r && m == s) ? V_.size() - 1 :
+                                    (
+                                    -24 - 50 * h - 35 * h2 - 10 * h3 - h4 - 36 * m - 12 * m2 + 12 * n + 70 * h * n +
+                                    30 * h2 * n + 4 * h3 * n + 24 * m * n - 12 * n2 - 30 * h * n2 - 6 * h2 * n2 + 4 * h * n3 +
+                                    44 * r - 48 * n * r + 12 * n2 * r + 24 * r2 - 12 * n * r2 + 4 * r3 + 24 * s) /
+                                    24;
+    }
+    std::vector<double> V_;
+    int                 N_;
+};
+
+class DPtableX
+{
+  public:
+    DPtableX() : V_(), N_(0), D_(0) {}
+    void resize(int d, int n)
+    {
+        N_         = n;
+        D_         = d;
+        int max_sz = 0;
+        for (int i = d; i < d + 3; ++i) max_sz = std::max(max_sz, (N_ - i) * (i - 5) * (i - 1) * (i - 2) / 2);
+        V_.resize(max_sz);
+    }
+    void          fill(const double& v) { std::fill(V_.begin(), V_.end(), v); }
+    double&       operator()(int i, int d, int e, int s) { return V_[index(i, d, e, s)]; }
+    const double& operator()(int i, int d, int e, int s) const { return V_[index(i, d, e, s)]; }
+    void          swap(DPtableX& x)
+    {
+        std::swap(V_, x.V_);
+        std::swap(N_, x.N_);
+        std::swap(D_, x.D_);
+    }
+
+  private:
+    int index(int i, int h1, int m1, int s) const
+    {
+        int d      = D_;
+        int d1d2   = (d - 1) * (d - 2);
+        int d5     = d - 5;
+        int h1_i_1 = h1 - i - 1;
+        assert(i + d < N_);
+        assert(d - 6 >= s);
+        assert(i < h1);
+        return i * d5 * d1d2 / 2 + s * d1d2 / 2 + h1_i_1 * (d - 1) - h1_i_1 * (h1 - i) / 2 + m1 - h1 - 1;
+    }
+
+    std::vector<double> V_;
+    int                 N_;
+    int                 D_;
+};
+
+#endif

+/*
+ * $Id$
+ *
+ * Copyright (C) 2008-2010 Kengo Sato
+ *
+ * This file comes from Ipknot.
+ */
+
+
+#include "fa.h"
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <cctype>
+#include <cstring>
+#include <cassert>
+
+typedef unsigned int uint;
+
+//static
+unsigned int Fasta::load(std::list<Fasta>& data, const char* file){
+
+  std::string line, name, seq, str;
+  std::ifstream ifs(file);
+  while (std::getline(ifs, line)) {
+    if (line[0]=='>') {         // header
+      if (!name.empty()) {
+        assert(str.size()==0 || seq.size()==str.size());
+        data.push_back(Fasta(name, seq, str));
+      }
+
+      name=line.substr(1);
+      seq.clear();
+      str.clear();
+      continue;
+    } 
+
+    if (std::strchr("()[].?xle ", line[0])==NULL) { // seq
+      uint i;
+      for (i=0; i!=line.size(); ++i)
+        if (!isalpha(line[i])) break;
+      seq+=line.substr(0, i);
+    } else {
+      uint i;
+      for (i=0; i!=line.size(); ++i)
+        if (std::strchr("()[].?xle ", line[i])==NULL) break;
+      str+=line.substr(0, i);
+    }
+  }
+  
+  if (!name.empty()) 
+    data.push_back(Fasta(name, seq, str));
+
+  return data.size();
+}
+

+/*
+ * $Id$
+ *
+ * Copyright (C) 2008-2010 Kengo Sato
+ *
+ * This file comes from Ipknot.
+*/
+
+#include <list>
+#include <string>
+
+using std::list;
+using std::string;
+
+class Fasta
+{
+  public:
+    Fasta() : name_(), seq_(), str_() {}
+    Fasta(const string& name, const string& seq, const string& str = "") : name_(name), seq_(seq), str_(str) {}
+    Fasta(const Fasta& fa) : name_(fa.name_), seq_(fa.seq_), str_(fa.str_) {}
+    Fasta& operator=(const Fasta& fa)
+    {
+        if (this != &fa) {
+            name_ = fa.name_;
+            seq_  = fa.seq_;
+            str_  = fa.str_;
+        }
+        return *this;
+    }
+    const string& name() const { return name_; }
+    const string& seq() const { return seq_; }
+    string&       seq() { return seq_; }
+    const string& str() const { return str_; }
+    unsigned int  size() const { return seq_.size(); }
+
+    static unsigned int load(list<Fasta>& data, const char* file);
+
+  private:
+    string name_;
+    string seq_;
+    string str_;
+};

+/*
+ * $Id$
+ *
+ * Copyright (C) 2010 Kengo Sato
+ *
+ * This file comes from IPknot.
+ *
+ */
+
+#include <boost/multi_array.hpp>
+#include <string>
+#include <vector>
+#include <iostream>
+
+using std::string;
+using std::vector;
+
+#define kB 0.00198717              // Boltzmann constant in kcal/mol/K
+#define ZERO_C_IN_KELVIN 273.15    // Zero degrees C in Kelvin
+#define AVOGADRO 6.022e23          // Avogadro's number
+
+typedef float energy_t;
+
+class DPtable2
+{
+  public:
+    DPtable2() : V_(), N_(0) {}
+    void resize(int n)
+    {
+        N_ = n;
+        V_.resize(N_ * (N_ + 1) / 2 + (N_ + 1));
+    }
+    void          fill(const float& v) { std::fill(V_.begin(), V_.end(), v); }
+    float&       operator()(int i, int j) { return V_[index(i, j)]; }
+    const float& operator()(int i, int j) const { return V_[index(i, j)]; }
+
+  private:
+    int index(int i, int j) const
+    {
+        assert(j <= N_);
+        return j == i - 1 ? N_ * (N_ + 1) / 2 + i : i * N_ + j - i * (1 + i) / 2;
+    }
+    std::vector<float> V_;
+    int                 N_;
+};
+
+class DPtable4
+{
+  public:
+    DPtable4() : V_(), N_(0) {}
+    void resize(int n)
+    {
+        N_ = n;
+        std::cout << V_.max_size() << " - " << N_ << " - " <<  sizeof(float) * static_cast<unsigned long>(N_) * (N_ - 1) * (N_ - 2) * (N_ - 3) / 2 / 3 / 4 << std::endl;
+        V_.resize(static_cast<unsigned long>(N_) * (N_ - 1) * (N_ - 2) * (N_ - 3) / 2 / 3 / 4); // This number can be HUGE
+        std::cout << "c'est toi qui bad_allocque ?" << std::endl;         
+    }
+    void          fill(const float& v) { std::fill(V_.begin(), V_.end(), v); }
+    float&       operator()(int i, int d, int e, int j) { return V_[index(i, d, e, j)]; }
+    const float& operator()(int i, int d, int e, int j) const { return V_[index(i, d, e, j)]; }
+
+  private:
+    int index(int h, int r, int m, int s) const
+    {
+        int n  = N_;
+        int h2 = h * h;
+        int h3 = h2 * h;
+        int h4 = h3 * h;
+        int m2 = m * m;
+        int n2 = n * n;
+        int n3 = n2 * n;
+        int r2 = r * r;
+        int r3 = r2 * r;
+        assert(h <= r);
+        assert(r <= m);
+        assert(m <= s);
+        assert(s <= N_);
+        return (h == r && m == s) ? V_.size() - 1 :
+                                    (
+                                    -24 - 50 * h - 35 * h2 - 10 * h3 - h4 - 36 * m - 12 * m2 + 12 * n + 70 * h * n +
+                                    30 * h2 * n + 4 * h3 * n + 24 * m * n - 12 * n2 - 30 * h * n2 - 6 * h2 * n2 + 4 * h * n3 +
+                                    44 * r - 48 * n * r + 12 * n2 * r + 24 * r2 - 12 * n * r2 + 4 * r3 + 24 * s) /
+                                    24;
+    }
+    std::vector<float> V_;
+    int                 N_;
+};
+
+class DPtableX
+{
+  public:
+    DPtableX() : V_(), N_(0), D_(0) {}
+    void resize(int d, int n)
+    {
+        N_         = n;
+        D_         = d;
+        int max_sz = 0;
+        for (int i = d; i < d + 3; ++i) max_sz = std::max(max_sz, (N_ - i) * (i - 5) * (i - 1) * (i - 2) / 2);
+        V_.resize(max_sz);
+    }
+    void          fill(const float& v) { std::fill(V_.begin(), V_.end(), v); }
+    float&       operator()(int i, int d, int e, int s) { return V_[index(i, d, e, s)]; }
+    const float& operator()(int i, int d, int e, int s) const { return V_[index(i, d, e, s)]; }
+    void          swap(DPtableX& x)
+    {
+        std::swap(V_, x.V_);
+        std::swap(N_, x.N_);
+        std::swap(D_, x.D_);
+    }
+
+  private:
+    int index(int i, int h1, int m1, int s) const
+    {
+        int d      = D_;
+        int d1d2   = (d - 1) * (d - 2);
+        int d5     = d - 5;
+        int h1_i_1 = h1 - i - 1;
+        assert(i + d < N_);
+        assert(d - 6 >= s);
+        assert(i < h1);
+        return i * d5 * d1d2 / 2 + s * d1d2 / 2 + h1_i_1 * (d - 1) - h1_i_1 * (h1 - i) / 2 + m1 - h1 - 1;
+    }
+
+    std::vector<float> V_;
+    int                 N_;
+    int                 D_;
+};
+
+class Nupack
+{
+  public:
+    Nupack();
+    void        load_sequence(const string& s);
+    void        load_parameters_fm363(const vector<float>& v);
+    void        load_default_parameters(/*int which*/);
+    bool        load_parameters(const char* filename);
+    void        dump_parameters(std::ostream& os) const;
+    float calculate_partition_function();
+    void        calculate_posterior();
+    void        get_posterior(vector<float>& bp, vector<int>& offset) const;
+    void        get_posterior(vector<float>& bp1, vector<float>& bp2, vector<int>& offset) const;
+
+  private:
+    void fastiloops(int i, int j, DPtable4& Qg, DPtableX& Qx, DPtableX& Qx2);
+    void fastiloops_pr(int i, int j, DPtable4& Qg, DPtableX& Qx, DPtableX& Qx2, DPtable4& Pg, DPtableX& Px, DPtableX& Px2);
+    energy_t score_hairpin(int i, int j) const;
+    energy_t score_loop(int l) const;
+    energy_t score_interior(int i, int d, int e, int j, bool pk) const;
+    energy_t score_interior_mismatch(int i, int j) const;
+    energy_t score_interior_mismatch(int i, int j, int k, int l) const;
+    energy_t score_interior_asymmetry(int l1, int l2) const;
+    energy_t score_multiloop(bool pk) const;
+    energy_t score_multiloop_paired(int n, bool pk) const;
+    energy_t score_multiloop_unpaired(int n, bool pk) const;
+    energy_t score_at_penalty(int i, int j) const;
+    energy_t score_dangle(int i, int j) const;
+    energy_t score_pk() const;
+    energy_t score_pk_multiloop() const;
+    energy_t score_pk_pk() const;
+    energy_t score_pk_paired(int n) const;
+    energy_t score_pk_unpaired(int n) const;
+    energy_t score_pk_band(int n) const;
+    int      base(char x) const;
+    bool     allow_paired(int i, int j) const;
+    bool     wc_pair(int i, int j) const;
+    int      pair_type(int i, int j) const;
+    int      pair_type(int i) const;
+
+    vector<int>                base_map;
+    boost::multi_array<int, 2> pair_map;
+    vector<int>                seq;
+    int                        N;
+    float                      RT;
+    DPtable2                   Q;
+    DPtable2                   Qb;
+    DPtable2                   Qm;
+    DPtable2                   Qp;
+    DPtable2                   Qz;
+    DPtable4                   Qg;
+    DPtable4                   Qgl;
+    DPtable4                   Qgr;
+    DPtable4                   Qgls;
+    DPtable4                   Qgrs;
+    DPtable2                   P;
+    DPtable2                   Pb;
+    DPtable2                   Pm;
+    DPtable2                   Pp;
+    DPtable2                   Pz;
+    DPtable2                   Pbg;
+    DPtable4                   Pg;
+    DPtable4                   Pgl;
+    DPtable4                   Pgr;
+    DPtable4                   Pgls;
+    DPtable4                   Pgrs;
+
+    // energy parameters
+    energy_t hairpin37[30];
+    energy_t bulge37[30];
+    energy_t interior37[30];
+    energy_t stack37[6][6];
+    energy_t int11_37[6][6][4][4];
+    energy_t int21_37[6][4][4][6][4];
+    energy_t int22_37[6][6][4][4][4][4];
+    energy_t dangle3_37[6][4];
+    energy_t dangle5_37[6][4];
+    energy_t triloop37[4][4][4][4][4];
+    energy_t tloop37[4][4][4][4][4][4];
+    energy_t mismatch_hairpin37[4][4][6];
+    energy_t mismatch_interior37[4][4][6];
+    energy_t asymmetry_penalty[4];
+    energy_t polyC_penalty, polyC_slope, polyC_int;
+    energy_t at_penalty;
+    energy_t multiloop_penalty;             // alpha1
+    energy_t multiloop_paired_penalty;      // alpha2
+    energy_t multiloop_unpaired_penalty;    // alpha3
+    energy_t pk_penalty;                    // beta1
+    energy_t pk_multiloop_penalty;          // beta1m
+    energy_t pk_pk_penalty;                 // beta1p
+    energy_t pk_paired_penalty;             // beta2
+    energy_t pk_unpaired_penalty;           // beta3
+    energy_t pk_band_penalty;
+    energy_t pk_stack_span;
+    energy_t pk_interior_span;
+    energy_t multiloop_penalty_pk;
+    energy_t multiloop_paired_penalty_pk;
+    energy_t multiloop_unpaired_penalty_pk;
+    energy_t max_asymmetry;
+    energy_t salt_correction;
+    energy_t loop_greater30;
+    energy_t hairpin_GGG;
+    float    intermolecular_initiation;
+};

+#include "rna.h"
+#include "nupack.h"
+#include <iostream>
+#include <string>
+#include <utility>
+#include <vector>
+
+using std::cout, std::cerr, std::endl;
+
+RNA::RNA(string name, string seq)
+{
+    if (!check_seq(seq)) {
+        cerr << "Unknown chars in input sequence. Please restrict to ACGTU." << endl;
+        exit(EXIT_FAILURE);
+    }
+    name_ = name;
+    seq_  = seq;
+    format();
+    n_ = seq_.size();
+    cout << "\t>formatted sequence" << endl;
+
+    /*define type_*/
+    type_ = vector<vector<int>>(n_, vector<int>(n_));
+    for (int i = 0; i < n_; i++) {
+        for (int j = 0; j < n_; j++) {
+            if (i < j) {
+                std::stringstream ss;
+                ss << seq_[i] << seq_[j];
+                string str = ss.str();
+                if (str.compare("AU") == 0) {
+                    type_[i][j] = 1;
+                } else if (str.compare("CG") == 0) {
+                    type_[i][j] = 2;
+
+                } else if (str.compare("GC") == 0) {
+                    type_[i][j] = 3;
+                } else if (str.compare("GU") == 0) {
+                    type_[i][j] = 4;
+                } else if (str.compare("UG") == 0) {
+                    type_[i][j] = 5;
+                } else if (str.compare("UA") == 0) {
+                    type_[i][j] = 6;
+                } else {
+                    type_[i][j] = 0;
+                }
+            } else {
+                type_[i][j] = 0;
+            }
+        }
+    }
+    nBP_ = type_.size();
+
+    /*define coord_*/
+    for (int i = 0; i < n_; i++) {
+        for (int j = 0; j < n_; j++) {
+            if (i < j and type_[i][j] > 0) {
+                if (i != 0 and i != n_ and j != 0 and j != n_) {
+                    if (type_[i - 1][j + 1] > 0 or type_[i + 1][j - 1] > 0) {
+                        coord_.push_back(std::make_pair(i, j));
+                    }
+                } else if (i == 0 or j == n_) {
+                    if (type_[i + 1][j - 1] > 0) {
+                        coord_.push_back(std::make_pair(i, j));
+                    }
+                }
+            }
+        }
+    }
+
+
+    /*define pij_*/
+    vector<float> bp;
+    vector<int>   offset;
+    Nupack        nu;
+    // nu.load_parameters("rna1999.dG");
+    nu.load_default_parameters();
+    cout << "\t>default parameters loaded (Serra and Turner, 1995)" << endl;
+    nu.load_sequence(seq_);
+    cout << "\t>computing pairing probabilities..." << endl;
+    try {
+        nu.calculate_partition_function();
+    } catch (std::exception& e) {
+        cerr << e.what() << endl;
+        exit(EXIT_FAILURE);
+    }
+    nu.calculate_posterior();
+    nu.get_posterior(bp, offset);
+
+    pij_ = vector<vector<float>>(n_, vector<float>(n_));
+    for (int i = 1; i <= n_; i++) {
+        for (int j = 1; j <= n_; j++) {
+            pij_[i - 1][j - 1] = bp[offset[i] + j];
+        }
+    }
+    cout << "\t>pairing probabilities defined" << endl;
+}
+
+int RNA::find_coord(pair<int, int> p)
+{
+    vector<pair<int, int>>::iterator it = find(coord_.begin(), coord_.end(), p);
+    int                              r  = -1;
+    if (it != coord_.end()) r = distance(coord_.begin(), it);
+    return r;
+}
+
+bool RNA::check_seq(string seq)    // Checks if the sequences only contains ACGUT.
+{
+    bool res = true;
+    for (unsigned int i = 0; i < seq.size(); i++) {
+        if (seq[i] != 'A' and seq[i] != 'U' and seq[i] != 'C' and seq[i] != 'G' and seq[i] != 'T') {
+            res = false;
+            break;
+        }
+    }
+    return res;
+}
+
+void RNA::format()
+{
+    for (unsigned int i = 0; i < seq_.size(); i++) {
+        seq_[i] = toupper(seq_[i]);
+        if (seq_[i] == 'T') {
+            seq_[i] = 'U';
+            break;
+        }
+    }
+}

+
+#ifndef DEF_RNA
+#define DEF_RNA
+
+#include <map>
+#include <string>
+#include <vector>
+
+using std::pair, std::string, std::vector, std::map;
+
+typedef struct Comp_ {
+    pair<uint, uint> pos;
+    int              score;
+    size_t           k;
+    Comp_(pair<int, int> p, int s) : pos(p), score(s) { k = 1 + pos.second - pos.first; }
+} Component;
+typedef struct {
+    string            atlas_id;
+    vector<Component> comp;
+    bool              reversed;
+} Motif;
+
+class RNA
+{
+  public:
+    RNA();
+    RNA(string name, string seq);
+
+    int                    get_n_();
+    string                 get_name_();
+    string                 get_seq_();
+    vector<vector<int>>    get_type_();
+    int                    get_type(int i, int j);
+    int                    get_type(int i);
+    vector<pair<int, int>> get_coord_();
+    pair<int, int>         get_coord(int i);
+    int                    get_coordF(int i);
+    int                    get_coordS(int i);
+    int                    find_coord(pair<int, int>);
+    vector<vector<float>>  get_pij_();
+    float                  get_pij(int i, int j);
+    float                  get_pij(int i);
+    int                    get_err_();
+    uint                   get_RNA_length() const;
+
+    bool check_seq(string seq);
+    void format();
+
+  private:
+    string                          name_;  /*name of the rna*/
+    string                          seq_;   /*sequence of the rna*/
+    int                             n_;     /*length of the rna*/
+    vector<vector<int>>             type_;  /*vector of base pair types*/
+    vector<pair<int, int>>          coord_; /*vector of base pair coordinates*/
+    vector<vector<float>>           pij_;   /*vector of probabilities*/
+    uint                            nBP_;   /*number of possible base pair*/
+};
+
+inline int                    RNA::get_n_() { return n_; }
+inline string                 RNA::get_name_() { return name_; }
+inline string                 RNA::get_seq_() { return seq_; }
+inline vector<vector<int>>    RNA::get_type_() { return type_; }
+inline int                    RNA::get_type(int i, int j) { return type_[i][j]; }
+inline int                    RNA::get_type(int i) { return type_[get_coord(i).first][get_coord(i).second]; }
+inline vector<pair<int, int>> RNA::get_coord_() { return coord_; }
+inline pair<int, int>         RNA::get_coord(int i) { return coord_[i]; }
+inline int                    RNA::get_coordF(int i) { return coord_[i].first; }
+inline int                    RNA::get_coordS(int i) { return coord_[i].second; }
+inline vector<vector<float>>  RNA::get_pij_() { return pij_; }
+inline float                  RNA::get_pij(int i, int j) { return pij_[i][j]; }
+inline float                  RNA::get_pij(int i) { return pij_[get_coord(i).first][get_coord(i).second]; }
+inline uint                   RNA::get_RNA_length() const { return nBP_; }
+
+#endif

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-#ifndef COMPONENT_H
-#define COMPONENT_H
-
-#include <string>
-
-class Component 
-{
-    public:
-        Component();
-        Component(std::string& cons_seq, uint k);
-    private:
-        std::string     _cons_seq;
-        uint            k;
-};
-
-
-istream& operator>>(istream& is, Component& m);
-ostream& operator<<(ostream& os, const Component& m);
-
-#endif
\ No newline at end of file

-#include "Motif.h"
\ No newline at end of file

-#ifndef MOTIF_H
-#define MOTIF_H
-
-#include <vector>
-#include <string>
-#include "Component.h"
-
-class Motif
-{
-    public:
-        Motif();
-        Motif(std::string filename);
-        ~Motif();
-        std::vector<Component>& getComponents() const;
-        Component& getComponent(uint k) const;
-        std::string name;
-
-    private:
-        std::vector<Component>  _comps;
-
-};
-
-istream& operator>>(istream& is, Motif& m);
-ostream& operator<<(ostream& os, const Motif& m);
-
-#endif
\ No newline at end of file

-#include "RNA.h"
-
-RNA::RNA() {}
-
-RNA::~RNA() {}
-
-RNA::RNA(std::string seq) : _seq(seq) { }

-#ifndef RNA_H
-#define RNA_H
-
-#include <string>
-
-class RNA {
-    public:
-        RNA();
-        RNA(std::string);
-        ~RNA();
-        uint            length() const;
-        std::string     str() const;
-        // char            seq(uint k) const;
-        // bool            isConsensus() const;
-        // bool            containsPseudoBases() const;
-    private:
-        std::string     _seq;
-        // bool            _coding;
-        // bool            _consensus;
-        // bool            _containsPseudoNTs;
-};
-
-inline uint RNA::length() const { return _seq.length(); }
-inline std::string RNA::str() const { return _seq; }
-
-#endif
\ No newline at end of file

-#include "Motif.h"
-#include <cstdlib>
-#include <iostream>
-#include <unistd.h>
-#include <boost/program_options.hpp>
-#include <boost/filesystem.hpp>
-
-#include "RNA.h"
-
-using namespace std;
-namespace bpo = boost::program_options;
-namespace bf = boost::filesystem;
-
-bool checkMotifFolder(bf::path & folder)
-{
-    if (not(bf::is_directory(folder) and bf::exists(folder))) return false;
-    bf::directory_iterator end_itr;
-    uint Ndesc = 0;
-    for (bf::directory_iterator itr(folder); itr != end_itr; ++itr)
-    {
-        if (itr->path().leaf().string().find(string(".desc")) != std::string::npos)
-            Ndesc++;
-    }
-    cout << "Found " << Ndesc << " .desc files in " << folder.string() << endl;
-    if (Ndesc > 0)
-        return true;
-    return false;
-}
-
-int parseMotifs(bf::path & folder)
-{
-    bf::directory_iterator end_itr;
-    for (bf::directory_iterator itr(folder); itr != end_itr; ++itr)
-    {
-        if (itr->path().leaf().string().find(string(".desc")) != std::string::npos)
-        {
-            
-        }
-    }
-
-}
-
-int main(int argc, char** argv)
-{
-    bf::path                    currentFolder(bf::current_path());
-    bf::path                    motifFolderPath(currentFolder); // By default, searching here...
-    bpo::options_description    desc("Options"); 
-    bpo::variables_map          options_map;
-    RNA                         querySequence;
-
-    desc.add_options() 
-      ("help", "Print this help message")
-      ("seq,s", bpo::value<string>()->required(), "RNA sequence to find motives in.")
-      ("motifs,m", bpo::value<bf::path>(), "Path to folder of DESC files describing the motifs to be used") 
-    ;
-    bpo::store(bpo::parse_command_line(argc, argv, desc), options_map);
-    bpo::notify(options_map);
-
-    if (options_map.count("help")) { 
-        cout << desc << endl; 
-        return EXIT_SUCCESS; 
-    } 
-    if (options_map.count("motifs")) {
-        motifFolderPath = options_map["motifs"].as<bf::path>();
-        if (not(checkMotifFolder(motifFolderPath))) { return EXIT_FAILURE; }
-    }
-    if (options_map.count("seq")) {
-        querySequence = RNA(options_map["seq"].as<string>());
-    }
-    cout << "Working with sequence " << querySequence.str() << " (length " << querySequence.length() << ")." << endl;
-
-    return EXIT_SUCCESS;
-}