secondaryStructureProcessor.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_SECONDARY_STRUCTURE_PROCESSOR_H
#define BALL_SECONDARY_STRUCTURE_PROCESSOR_H

#ifndef  BALL_COMMON_H
#include <BALL/common.h>
#endif

#ifndef BALL_CONCEPT_COMPOSITE_H
# include <BALL/CONCEPT/composite.h>
#endif

#include <vector>

namespace BALL
{
  class SecondaryStructure;
    
  class BALL_EXPORT SecondaryStructureProcessor 
    : public UnaryProcessor<Composite>
  {
    public:


    SecondaryStructureProcessor();


    virtual Processor::Result operator() (Composite& composite);

    protected:

    void compute_();

    // helper function for finish()
    char setSecondaryStructureType_(SecondaryStructure* ss, char type);

    bool testString_(const String& s, Size offset, Size offset_2);
    bool testString2_(const String& s, Size offset);
    bool testString3_(const String& s, Size offset, char x);
      
    void insertTurn_(int turn, int position);
    void changeAllXToY_(char X, char Y, String& target);      

    // matrix to save the possible HBondPairs
    std::vector<std::vector<Position> > HBonds_;

    //vector to save the bridges
    std::vector<std::vector<int> > posbridges_; 

    String sheet_;
    String fiveturn_;
    String fourturn_;
    String threeturn_;
    String summary_;
  };

} //namespace BALL

#endif // BALL_STRUCTURE_SECONDARYSTRUCTUREPROCESSOR_H

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