PredictionTrackerProfileMinE.h

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#ifndef INTARNA_PREDICTIONTRACKERPROFILEMINE_H_
#define INTARNA_PREDICTIONTRACKERPROFILEMINE_H_
 
#include "IntaRNA/PredictionTracker.h"
#include "IntaRNA/InteractionEnergy.h"
 
#include <iostream>
 
#include <boost/algorithm/string.hpp>
 
namespace IntaRNA {
 
class PredictionTrackerProfileMinE: public PredictionTracker
{
 
public:
 
    PredictionTrackerProfileMinE(
                const InteractionEnergy & energy
                , const std::string & seq1streamName
                , const std::string & seq2streamName
                , const std::string & E_INF_string = "NA"
                , const std::string & sep = ";"
            );
 
    PredictionTrackerProfileMinE(
                const InteractionEnergy & energy
                , std::ostream * seq1stream
                , std::ostream * seq2stream
                , const std::string & E_INF_string = "NA"
                , const std::string & sep = ";"
            );
 
    virtual ~PredictionTrackerProfileMinE();
 
 
    virtual
    void
    updateOptimumCalled( const size_t i1, const size_t j1
                        , const size_t i2, const size_t j2
                        , const E_type energy
                        );
 
 
protected:
 
    const InteractionEnergy & energy;
 
    const bool deleteStreamsOnDestruction;
 
    std::ostream * seq1stream;
 
    std::ostream * seq2stream;
 
    const std::string E_INF_string;
 
    const std::string sep_string;
 
    typedef std::vector<E_type> MinEProfile;
 
    MinEProfile seq1minE;
 
    MinEProfile seq2minE;
 
    static
    void
    updateProfile(    MinEProfile & profile
                    , const size_t i
                    , const size_t j
                    , const E_type E);
 
    template < typename MinEProfileIterator >
    static
    void
    writeProfile( std::ostream &out
                , const MinEProfileIterator & begin
                , const MinEProfileIterator & end
                , const RnaSequence & rna
                , const std::string & E_INF_string
                , const std::string & sep_string
                );
 
 
};
 
 
template < typename MinEProfileIterator >
inline
void
PredictionTrackerProfileMinE::
writeProfile( std::ostream &out
            , const MinEProfileIterator & begin
            , const MinEProfileIterator & end
            , const RnaSequence & rna
            , const std::string & E_INF_string
            , const std::string & sep_string
            )
{
    // write in CSV-like format (column data)
 
    // print header : seq.ID ; minE
    out <<"idx"<<sep_string<<boost::replace_all_copy(rna.getId(), sep_string, "_")<<sep_string<<"minE" <<'\n';
    // print minE data
    size_t i=0;
    for (MinEProfileIterator curE = begin; curE!=end; curE++) {
        out
            // out index
            <<rna.getInOutIndex(i)<<sep_string
            // out nucleotide (index starts with 0)
            <<rna.asString().at(i)<<sep_string
            ;
        // out infinity replacement if needed
        if ( E_isINF( *curE ) ) {
            out<<E_INF_string <<'\n';
        } else {
            out <<E_2_Ekcal(*curE) <<'\n';
        }
        // increase position counter
        i++;
    }
}
 
 
} // namespace
 
#endif /* PREDICTIONTRACKERPROFILEMINE_H_ */