fmindex_inl.h File Reference

Go to the source code of this file.

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.

Functions
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	nvbio::rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, uint8 c)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, uint8 c)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE TRankDictionary::vec4_type	nvbio::rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename TRankDictionary::vec4_type *outl, typename TRankDictionary::vec4_type *outh)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *out)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outl, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outh)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type in_range)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::match_reverse (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	nvbio::basic_inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	nvbio::locate (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	nvbio::locate_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	nvbio::lookup_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type it)