/usr/include/oxli/assembler.hh

/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2015-2016, The Regents of the University of California.

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    * Redistributions in binary form must reproduce the above
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      of its contributors may be used to endorse or promote products
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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Contact: khmer-project@idyll.org
*/
#ifndef ASSEMBLER_HH
#define ASSEMBLER_HH

#include <functional>

#include "oxli.hh"
#include "kmer_hash.hh"
#include "hashgraph.hh"
#include "kmer_filters.hh"
#include "traversal.hh"
#include "labelhash.hh"


namespace oxli
{

class Hashgraph;
class LabelHash;

/**
 * \class LinearAssembler
 *
 * \brief Naively assemble linear paths.
 *
 * The LinearAssember is the basic building block of general assembly.
 * The core function, _assemble_directed, takes a direction and branch-specialiazed
 * AssemblerTraverser and gathers a contig up until any branch points. The behavior
 * of this function can be modified by passing it a cursor with varying
 * filtering functions.
 *
 * The assemble, assemble_right, and assemble_left functions are for convenience.
 * They take care of building the filters and creating the contig strings.
 *
 * \author Camille Scott
 *
 * Contact: camille.scott.w@gmail.com
 *
 */
class LinearAssembler
{
public:

    WordLength _ksize;
    const Hashgraph * graph;

    explicit LinearAssembler(const Hashgraph * ht);

    virtual std::string assemble(const Kmer seed_kmer,
                                 const Hashgraph * stop_bf = 0) const;

    virtual std::string assemble_right(const Kmer seed_kmer,
                                       const Hashgraph * stop_bf = 0) const;

    virtual std::string assemble_left(const Kmer seed_kmer,
                                      const Hashgraph * stop_bf = 0) const;

    template <bool direction>
    std::string _assemble_directed(AssemblerTraverser<direction>& cursor) const;
};

// The explicit specializations need to be declared in the same translation unit
// as their unspecialized declaration.
template<>
std::string LinearAssembler::_assemble_directed<TRAVERSAL_LEFT>(AssemblerTraverser<TRAVERSAL_LEFT>
        &cursor) const;

template<>
std::string LinearAssembler::_assemble_directed<TRAVERSAL_RIGHT>(AssemblerTraverser<TRAVERSAL_RIGHT>
        &cursor) const;


/**
 * \class SimpleLabeledAssembler
 *
 * \brief Assemble linear paths using labels to span high degree nodes.
 *
 * Shares a common API (namely, the assemble and templated _assemble_directed functions) with
 * LinearAssembler, though does not inherit. High degree nodes (nodes with degree > 2) are spanned
 * using labeling formation: if there is a matching label on two sides of the HDN, we can keep
 * traverse across. Internally, this is performed by pushing a new filter to search for the label on to
 * the Traverser's filter stack and popping it on the other side of the HDN. This implementation also
 * does a simple check to guess whether a branch is an error: if the HDN has label coverage great than 5, and
 * the branch has only a single label spanning, it is guessed to be a tip and ignored.
 *
 * \author Camille Scott
 *
 * Contact: camille.scott.w@gmail.com
 *
 */
class SimpleLabeledAssembler
{
    const LinearAssembler * linear_asm;

public:

    const Hashgraph * graph;
    const LabelHash * lh;
    WordLength _ksize;

    explicit SimpleLabeledAssembler(const LabelHash * lh);
    ~SimpleLabeledAssembler();

    StringVector assemble(const Kmer seed_kmer,
                          const Hashgraph * stop_bf=0) const;

    template <bool direction>
    void _assemble_directed(AssemblerTraverser<direction>& start_cursor,
                            StringVector& paths) const;

};


class JunctionCountAssembler
{
    LinearAssembler linear_asm;
    Countgraph * junctions;
    Traverser traverser;

public:

    Hashgraph * graph;
    WordLength _ksize;

    explicit JunctionCountAssembler(Hashgraph * ht);
    ~JunctionCountAssembler();


    StringVector assemble(const Kmer seed_kmer,
                          const Hashtable * stop_bf=0) const;

    uint16_t consume(std::string sequence);
    void count_junction(Kmer kmer_a, Kmer kmer_b);
    BoundedCounterType get_junction_count(Kmer kmer_a, Kmer kmer_b) const;

    template <bool direction>
    void _assemble_directed(AssemblerTraverser<direction>& start_cursor,
                            StringVector& paths) const;

};
} //namespace oxli
#endif
liboxli-dev 2.1.2+dfsg-3 / usr / include / oxli / assembler.hh
