fmindex.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/fmindex/rank_dictionary.h>
#include <nvbio/strings/string_traits.h>
#include <nvbio/fmindex/fmindex_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::fm_index< TRankDictionary, TSuffixArray, TL2 >

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 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 >
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 >::range_type i)