Kmer< span >::KmerMinimizer< Model, Comparator > Class Template Reference

Kmer type for the ModelMinimizer class. More...

#include <Model.hpp>

Inherits Kmer.

Public Member Functions
const Model::Kmer &	minimizer () const
int	position () const
bool	hasChanged () const

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN>
template<class Model, class Comparator>
class gatb::core::kmer::impl::Kmer< span >::KmerMinimizer< Model, Comparator >

Kmer type for the ModelMinimizer class.

This class associates a kmer and its minimizer. It inherits from the Model::Kmer type and adds methods specific to minimizers, such as minimizer itself (ie the Model::Kmer object holding the minimizer), position giving the position of the minimizer whithin the kmer and hasChanged telling whether a minimizer has changed during iteration of kmers from some data source (a sequence data for instance).

NOTE: this class is not intended to be used directly by end users. Instead, the typedef definition ModelMinimizer::Kmer should be preferred.

Example of use:

        // We declare a kmer model with kmer size big enough to represent our sequence.
        // Note that we give a second size, which is the size of the minimizers
        ModelMinimizer model (kmerSize, 8);

        // We get a reference on the minimizer model, which will be useful for dumping
        // string value of a minimizer. Recall that 'model' is a model configured with
        // 'kmerSize' but has also to deal with mmers of size kmerSize/2. The 'getMmersModel'
        // method just provides access to this inner model.
        const ModelCanonical& modelMinimizer = model.getMmersModel();

        // We compute the kmer for a given sequence
        ModelMinimizer::Kmer kmer = model.codeSeed (seq, Data::ASCII);

        std::cout << std::endl;
        std::cout << "-------------------- MINIMIZER --------------------" << std::endl;
        std::cout << "kmer  value is: " << kmer.value()                    << std::endl;
        std::cout << "kmer string is: " << model.toString(kmer.value())    << std::endl;

        // With this model, we have extra information.
        std::cout << "forward value  is: " << kmer.forward()                    << std::endl;
        std::cout << "forward string is: " << model.toString(kmer.forward())    << std::endl;
        std::cout << "revcomp value  is: " << kmer.revcomp()                    << std::endl;
        std::cout << "revcomp string is: " << model.toString(kmer.revcomp())    << std::endl;
        std::cout << "used strand is   : " << toString(kmer.strand())           << std::endl;

        // We can also have information about minimizers.
        // Note :  kmer.minimizer() is of type ModelCanonical, ie the type provided as
        // template argument of the ModelMinimizer class.
        std::cout << "minimizer model size       : " << modelMinimizer.getKmerSize() << std::endl;
        std::cout << "minimizer value is         : " << kmer.minimizer().value()     << std::endl;
        std::cout << "minimizer string is        : " << modelMinimizer.toString(kmer.minimizer().value()) << std::endl;
        std::cout << "minimizer position in kmer : " << kmer.position()   << std::endl;
        std::cout << "minimizer changed          : " << kmer.hasChanged() << std::endl;

Member Function Documentation

bool hasChanged ( ) const

inline

Tells whether the minimizer has changed; useful while iterating kmers

Returns

true if changed, false otherwise

const Model::Kmer& minimizer ( ) const

inline

Returns the minimizer of the current kmer as a Model::Kmer object

Returns

the Model::Kmer instance

int position ( ) const

inline

Returns the position of the minimizer within the kmer. By convention, a negative value means that there is no minimizer inside the kmer.

Returns

the position of the minimizer.

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The documentation for this class was generated from the following file:

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/kmer/impl/Model.hpp