This class can compute a form of alignment with a slightly more complicated cost function than LinearAligner. More...

#include <musaline.hpp>

Public Types
typedef CostCalc	CostCalculator

Public Member Functions
	AffineAligner (CostCalculator ccal=CostCalculator())
	Constructor. More...

void	set_cost_calculator (CostCalculator ccal)
	Set a different CostCalculator object.

CostCalculator const &	get_cost_calculator () const
	Get a const reference to the current CostCalculator object.

template<class Sequence0 , class Sequence1 >
Alignment	global_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	cut_one_end_off_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	cut_one_begin_off_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	inside_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	initial_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	end_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	semi_align (Sequence0 const &seq0, Sequence1 const &seq1) const

template<class Sequence0 , class Sequence1 >
Alignment	partial_align (Sequence0 const &seq0, Sequence1 const &seq1) const
	No requirement for start and end.

Detailed Description

template<class CostCalc>
class musaline::AffineAligner< CostCalc >

This class can compute a form of alignment with a slightly more complicated cost function than LinearAligner.

An element of a sequence can be aligned with an element of the other sequence or with a gap. The cost of aligning two elements or an element does not depend on the context, but the cost of extending a gap can be different from starting a gap.

The class has several align functions which differ in what part of the sequences should be aligned. Details are provided with the individual align functions.

This class takes a CostCalculator class as a template parameter. This class shall be provided by the user and gives the benefit of matching one element with another one. If you can call the following function template with your cost calculator and sequences, you should be OK. More detailed requirements are listed after the function.

#include "boost/range.hpp"
    template <class CostCalculator, class Sequence0, class Sequence1>
    void affine_usage(CostCalculator const &ccal,
            Sequence0 const &seq0, Sequence1 const &seq1)
    {
        // Copy constructor
        CostCalculator ccal_copy(ccal);
        // assignment operator
        ccal_copy = ccal;
        ccal.preprocess(seq0, seq1);
        double d = ccal.gap_bft();
        d = ccal.ext_bft();
        size_t sz0 = boost::distance(seq0);
        size_t sz1 = boost::distance(seq1);
        auto s0cur = boost::const_begin(seq0);
        for (size_t i=0; i!=sz0; ++i) {
            auto s1cur = boost::const_begin(seq1));
            for (size_t j=0; j!=sz1; ++j) {
                double benefit = ccal.match(*s0cur, *s1cur);
                ++s1cur;
            }
            ++s0cur;
        }
    }

The classes Sequence0 and Sequence1 should fulfill the requirements for a boost Forward Range. See the documentation of the range library on http://www.boost.org for full details. A range can be thought of as a 'container light'. It should give access to a begin and end iterator, which should be forward iterators.

The CostCalculator class has the same requirements as the CostCalculator for the LinearAligner class, plus one extra required member function:

ext_bft. Returns the benefit for extending a gap, that is, for matching an element with a gap, where the previous element was also matched with a gap. The returned value should be negative, otherwise, the results are not guaranteed to be the optimal solution.

Constructor & Destructor Documentation

template<class CostCalc >

musaline::AffineAligner< CostCalc >::AffineAligner ( CostCalculator ccal = CostCalculator() )

inline

Constructor.