NucleotideLinker.h

#ifndef NLINK
#define NLINK

//#include <GL/glut.h>
#include <QtOpenGL/QGLWidget>
#include <vector>
#include <string>
#include <list>
#include <map>
#include <algorithm>
#include <math.h>
#include "NucleotideLink.h"

#define PI 3.141592653589793

using namespace std;

class NucleotideLinker
{
public:
    int F_width;
    int min_width;
    vector<NucleotideLink> links;

    NucleotideLinker();
    /*
    inline NucleotideLink operator[] (int index)
    {
        return link_map[ (index/8) * 8 ];//round down index
    }*/

    void display();

    void calculate(string sequence, int min = 200);

    vector<float> smooth( int preferred_width, int blur_size);

    //	void tie_up_loose_ends(vector<float>& width_list);
private:
    void draw_arc(int distance);

    void DrawArc(float r, float cx = 0, float cy = 0, float start_angle = PI, float arc_angle= PI, int num_segments = 0);

    NucleotideLink multiples_check(const string& seq, NucleotideLink match, int consensus_width);

    NucleotideLink localized_search(const string& seq, int start, int dist, unsigned int range);

    void check_for_max(const string& seq, int dist, int index, short int& max, int& best_distance);

    float average( const list<int>& window );

};



#endif