BioDnaSequenceDotPlot.h

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#ifndef BIODNASEQUENCEDOTPLOT_H
#define BIODNASEQUENCEDOTPLOT_H

#include "BioDnaSequence.h"
#include "BioFasta.h"
#include "BioDnaSubstitutionMatrix.h"
#include "BioLenPos.h"
#include "BioEmbl.h"
#include "BioGenBank.h"
#include "BioPostScript.h"

class BioDnaSequenceDotPlot
{
  private :
                 string seq1;
                 string seq2;
                 string nameSeq1_;
                 string nameSeq2_;
                 string graphLabel_;

                 unsigned int windowSize_,stringency_;
                 
                 float r_,g_,b_;
                 
//                 void ParseMatrix();
                 int compare(string str1,string str2,unsigned int s);

  public  :
    BioDnaSequenceDotPlot(){}

    BioDnaSequenceDotPlot(BioDnaSequence,BioDnaSequence,string="IDENTITY");
    BioDnaSequenceDotPlot(BioDnaSequence,string,string="IDENTITY");

    BioDnaSequenceDotPlot(BioEmbl,BioEmbl,string="IDENTITY");
    BioDnaSequenceDotPlot(BioEmbl,string,string="IDENTITY");

    BioDnaSequenceDotPlot(BioGenBank,BioGenBank,string="IDENTITY");
    BioDnaSequenceDotPlot(BioGenBank,string,string="IDENTITY");

    
    BioDnaSequenceDotPlot(BioFasta,BioFasta,string="IDENTITY");
    BioDnaSequenceDotPlot(BioFasta,string,string="IDENTITY");

    BioDnaSequenceDotPlot(string,string,string="IDENTITY");

    void showDotPlot(BioPostScript& ps,unsigned int startX_=80,unsigned int startY_=200,unsigned int size_=500);
    void setPlotColor(unsigned int r,unsigned int g, unsigned int b);
    void setLabels (string,string,string);
    void setWindowSize(unsigned int windowSize);
    void setStringency(unsigned int stringency);
};

#endif