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Add a few useful types and functions to UnitigMap #19

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21 changes: 17 additions & 4 deletions src/UnitigMap.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ template<typename U, typename G> class CompactedDBG;
template<typename U, typename G, bool is_const> class BackwardCDBG;
template<typename U, typename G, bool is_const> class ForwardCDBG;
template<typename U, typename G, bool is_const> class neighborIterator;
template<typename U, typename G, bool is_const> struct UnitigMapHash;

/** @class UnitigMapBase
* @brief Structure containing the basic information of a unitig mapping. This structure is independent
Expand Down Expand Up @@ -99,6 +100,7 @@ class UnitigMap : public UnitigMapBase {
template<typename U, typename G, bool C> friend class ForwardCDBG;
template<typename U, typename G, bool C> friend class unitigIterator;
template<typename U, typename G, bool C> friend class UnitigMap;
template<typename U, typename G, bool C> friend class UnitigMapHash;

typedef typename std::conditional<is_const, const CompactedDBG<U, G>*, CompactedDBG<U, G>*>::type CompactedDBG_ptr_t;
typedef typename std::conditional<is_const, const U*, U*>::type Unitig_data_ptr_t;
Expand All @@ -108,6 +110,9 @@ class UnitigMap : public UnitigMapBase {
typedef BackwardCDBG<U, G, is_const> UnitigMap_BW;
typedef ForwardCDBG<U, G, is_const> UnitigMap_FW;

using hasher = UnitigMapHash<U, G, is_const>;
using neighbor_iterator = neighborIterator<U, G, is_const>;

/** UnitigMap constructor.
* @param length is the length of the mapping in k-mers (default is 1 k-mer).
* @param cdbg_ is a pointer to the CompactedDBG containing the reference unitig used for the mapping (default is nullptr).
Expand Down Expand Up @@ -152,6 +157,14 @@ class UnitigMap : public UnitigMapBase {
*/
string referenceUnitigToString() const;

/**
* By default, cdbg->find returns a mapping of a single k-mer on a unitig. This function makes a copy of this
* object, but where the mapping represents the full unitig.
*/
UnitigMap<U, G, is_const> mappingToFullUnitig() const;

bool isFullMapping() const;

/** Compute the length of the longest common prefix between a given sequence and
* the reference unitig used in the mapping.
* @param s is a pointer to an array of characters representing the sequence from
Expand Down Expand Up @@ -262,11 +275,11 @@ class UnitigMap : public UnitigMapBase {

UnitigMap(size_t p_unitig, size_t i, size_t l, size_t sz, bool short_, bool abundance, bool strd, CompactedDBG_ptr_t cdbg_);

neighborIterator<U, G, is_const> bw_begin() const;
neighborIterator<U, G, is_const> bw_end() const;
neighbor_iterator bw_begin() const;
neighbor_iterator bw_end() const;

neighborIterator<U, G, is_const> fw_begin() const;
neighborIterator<U, G, is_const> fw_end() const;
neighbor_iterator fw_begin() const;
neighbor_iterator fw_end() const;

template<bool is_void> typename std::enable_if<!is_void, Unitig<U>>::type splitData_(const bool last_split) const;
template<bool is_void> typename std::enable_if<is_void, Unitig<U>>::type splitData_(const bool last_split) const;
Expand Down
14 changes: 14 additions & 0 deletions src/UnitigMap.tcc
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Expand Up @@ -64,6 +64,20 @@ string UnitigMap<U, G, is_const>::referenceUnitigToString() const {
return cdbg->v_unitigs[pos_unitig]->getSeq().toString();
}

template<typename U, typename G, bool is_const>
UnitigMap<U, G, is_const> UnitigMap<U, G, is_const>::mappingToFullUnitig() const {
UnitigMap<U, G, is_const> cpy(*this);
cpy.dist = 0;
cpy.len = size - cdbg->getK() + 1;

return cpy;
}

template<typename U, typename G, bool is_const>
bool UnitigMap<U, G, is_const>::isFullMapping() const {
return !isEmpty && dist == 0 && len == size - getGraph()->getK() + 1;
}

template<typename U, typename G, bool is_const>
size_t UnitigMap<U, G, is_const>::lcp(const char* s, const size_t pos_s, const size_t pos_um_seq, const bool um_reversed) const {

Expand Down