Accessibility.h

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#ifndef INTARNA_ACCESSIBILITY_H_
#define INTARNA_ACCESSIBILITY_H_
 
 
#include "IntaRNA/general.h"
#include "IntaRNA/RnaSequence.h"
#include "IntaRNA/IndexRangeList.h"
#include "IntaRNA/AccessibilityConstraint.h"
 
#include <stdexcept>
 
namespace IntaRNA {
 
template<class T> class UpperBandedMatrix;
 
class Accessibility {
 
public:
 
    const static E_type ED_UPPER_BOUND;
 
public:
 
    Accessibility( const RnaSequence& sequence
                    , const size_t maxLength
                    , const AccessibilityConstraint * const accConstr
                );
 
    virtual ~Accessibility();
 
    virtual
    E_type
    getED( const size_t from, const size_t to ) const = 0;
 
    virtual
    const RnaSequence &
    getSequence() const;
 
    virtual
    size_t
    getMaxLength() const;
 
    virtual
    const AccessibilityConstraint&
    getAccConstraint() const;
 
    void
    writeRNAplfold_Pu_text( std::ostream& out, const Z_type RT ) const;
 
    void
    writeRNAplfold_ED_text( std::ostream& out ) const;
 
    virtual void writeBinary( std::ostream & out ) const;
 
    friend std::ostream& operator<<(std::ostream& out, const Accessibility& acc);
 
    IndexRangeList
    decomposeByMaxED( const size_t maxRangeLength
                    , const size_t winSize
                    , const size_t minRangeLength ) const;
 
 
    void
    decomposeByMaxED( IndexRangeList & ranges, const E_type maxED, const size_t minRangeLength ) const;
 
protected:
 
    void writeBinary( std::ostream & out, const UpperBandedMatrix<E_type> * matrix ) const;
 
    const RnaSequence & seq;
 
    const size_t maxLength;
 
    AccessibilityConstraint accConstraint;
 
    virtual
    void
    checkIndices( const size_t from, const size_t to ) const;
 
    void
    writeRNAplfold_text( std::ostream& out, const Z_type RT, const bool writeProbs ) const;
 
};
 
 
 
 
inline
Accessibility::Accessibility( const RnaSequence& seq
                            , const size_t maxLength
                            , const AccessibilityConstraint * const accConstraint_ )
 :
    seq(seq)
    // set maxLength to appropriate value
    , maxLength( maxLength==0 ? seq.size() : std::min(maxLength,seq.size()) )
    , accConstraint( seq.size(), 0, "", "", "" )
{
    // set constraint if needed
    if (accConstraint_ != NULL) {
        accConstraint = *accConstraint_;
    }
}
 
 
inline
Accessibility::~Accessibility()
{
}
 
 
inline
void
Accessibility::
checkIndices( const size_t from, const size_t to ) const
{
#if INTARNA_IN_DEBUG_MODE
    if (from > to || to >= getSequence().size()) {
        throw std::runtime_error("Accessibility::checkIndices : region ["+toString(from)+","+toString(to)+"] does not fulfill 0 <= from <= to < seq.length");
    }
#endif
}
 
 
inline
const RnaSequence &
Accessibility::
getSequence() const
{
    return seq;
}
 
 
inline
size_t
Accessibility::
getMaxLength() const
{
    return maxLength;
}
 
 
inline
const AccessibilityConstraint&
Accessibility::
getAccConstraint() const
{
    return accConstraint;
}
 
 
inline
void
Accessibility::
writeRNAplfold_ED_text( std::ostream& out ) const
{
    writeRNAplfold_text( out, 1.0, false );
}
 
 
inline
void
Accessibility::
writeRNAplfold_Pu_text( std::ostream& out, const Z_type RT ) const
{
    writeRNAplfold_text( out, RT, true );
}
 
 
}
 
#endif /* ACCESSIBILITY_H_ */