RepeatOverviewDisplay.h

//RepeatOverviewDisplay.h
#ifndef ALIGNMENT_DISP
#define ALIGNMENT_DISP

#include <QtOpenGL/QGLWidget>
#include <vector>
#include "BasicTypes.h"
#include "UiVariables.h"
#include "NucleotideDisplay.h"

using namespace std;

class RepeatOverviewDisplay : public NucleotideDisplay
{
    Q_OBJECT
    
public:

    RepeatOverviewDisplay(UiVariables*, GLWidget* gl);
    void checkVariables();
    void calculateOutputPixels();
    void display();
    int width();
    void displayLegend(float canvasWidth, float canvasHeight);
    color alignment_color(int score, int frequency);
    color interpolate(color p1, color p3, double progress);

    /** Optimized Long Int Accessors*/
    long int& accessLI(int index);
    long int sequenceLI(int index);
    int countMatches(long int bits);

    /** Optimized Packed Sequence Methods*/
    int countMatchesShort(unsigned short int bits);
    int countMatchesChar(unsigned char bits);
    void calcMatchTable();
    void normalPack(const string* seq);
    void shiftMask(char* str, int size);
    void shiftString(unsigned char* str, int size);
    color simpleAlignment(int index);
    pair<int,int> getBestAlignment(int index);
    void setSequence(const string* seq);

    /** Mouse Click methods */
    string SELECT_StringFromMouseClick(int index);
    string FIND_StringFromMouseClick(int index);
    int getRelativeIndexFromMouseClick(point2D pt);

public slots:
    void changeScale(int s);
    void toggleVisibility();

protected:
    int internalScale;

private:	
    unsigned int charPerIndex;
    int* countTable;
    int* countTableShort;
    int* countTableChar;
    unsigned char* packSeq;
    int pSeqSize;
    int legendWidth;

    GLuint display_object;
    GLWidget* glWidget;

};

inline
long int& RepeatOverviewDisplay::accessLI(int index)
{
    unsigned char* ptr = &(packSeq[pSeqSize - index - sizeof(long int)]);
    return  *( (long int*)(ptr) );
}

inline
long int RepeatOverviewDisplay::sequenceLI(int index)
{
    int sub_index = index % charPerIndex;
    index /= charPerIndex;

    long int start = accessLI(index);
    if(sub_index)//skip all the shifting if we don't have to do it
    {
        int inc = sub_index * 2;
        start = start << inc;
        unsigned long int end = accessLI(index + sizeof(long int) );//sign bit has a bad tendency to get duplicated
        end = end >> (32 - inc);
        start += end;
    }
    return start;
}

inline
int RepeatOverviewDisplay::countMatches(long int bits)
{
    //TODO: can I do this by pointer casting?
    int c = countTable[ (unsigned short int)bits ];
    unsigned short int b = bits >> 16;
    c += countTable[ b ];

    return c;
}


#endif