PredictionTrackerProfileSpotProb.h

Go to the documentation of this file.

 
#ifndef INTARNA_PREDICTIONTRACKERPROFILESPOTPROB_H_
#define INTARNA_PREDICTIONTRACKERPROFILESPOTPROB_H_
 
#include "IntaRNA/PredictionTracker.h"
#include "IntaRNA/InteractionEnergy.h"
 
#include <iostream>
 
#include <boost/algorithm/string.hpp>
 
namespace IntaRNA {
 
class PredictionTrackerProfileSpotProb: public PredictionTracker
{
 
public:
 
    PredictionTrackerProfileSpotProb(
                const InteractionEnergy & energy
                , const std::string & seq1streamName
                , const std::string & seq2streamName
                , const std::string & NA_string = "NA"
                , const std::string & sep = ";"
            );
 
    PredictionTrackerProfileSpotProb(
                const InteractionEnergy & energy
                , std::ostream * seq1stream
                , std::ostream * seq2stream
                , const std::string & NA_string = "NA"
                , const std::string & sep = ";"
            );
 
    virtual ~PredictionTrackerProfileSpotProb();
 
 
    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 NA_string;
 
    const std::string sep;
 
    typedef std::vector<Z_type> ZProfile;
 
    ZProfile seq1Z;
 
    ZProfile seq2Z;
 
    Z_type overallZ;
 
    static
    void
    updateProfile(    ZProfile & profile
                    , const size_t i
                    , const size_t j
                    , const Z_type boltzmannWeight);
 
    template < typename ZProfileIterator >
    static
    void
    writeProfile( std::ostream &out
                , const ZProfileIterator & begin
                , const ZProfileIterator & end
                , const Z_type overallZ
                , const RnaSequence & rna
                , const std::string & NA_string
                , const std::string & sep
                );
 
 
};
 
 
template < typename ZProfileIterator >
inline
void
PredictionTrackerProfileSpotProb::
writeProfile( std::ostream &out
            , const ZProfileIterator & begin
            , const ZProfileIterator & end
            , const Z_type overallZ
            , const RnaSequence & rna
            , const std::string & NA_string
            , const std::string & sep
            )
{
    // write in CSV-like format (column data)
 
    const bool noZ = (overallZ==0.0);
 
    // print header : seq.ID ; spotProb
    out <<"idx"<<sep<<boost::replace_all_copy(rna.getId(), sep, "_")<<sep<<"spotProb" <<'\n';
    // print spot probability data
    size_t i=0;
    for (ZProfileIterator curZ = begin; curZ!=end; curZ++) {
        out
            // out index
            <<rna.getInOutIndex(i)<<sep
            // out nucleotide (index starts with 0)
            <<rna.asString().at(i)<<sep
            ;
        // out infinity replacement if needed
        if ( noZ || Z_isINF( *curZ ) ) {
            out<<NA_string <<'\n';
        } else {
            out <<((*curZ)/overallZ) <<'\n';
        }
        // increase position counter
        i++;
    }
}
 
 
} // namespace
 
#endif /* PREDICTIONTRACKERPROFILESPOTPROB_H_ */