When re-mapping fid_Sequences::sspfile or fid_Sequences::sdsfile, always remember to set fid_Sequences::descriptions and fid_Sequences::separator, respectively, to the corresponding content pointer since this might have changed after the re-mapping.
Definition at line 36 of file sequences.h.
#include <sequences.h>
Data Fields | |
fid_Uintsize | uisize |
Integer size. | |
const fid_Alphabet * | alpha |
Reference to the alphabet the sequence data is encoded with. | |
fid_Uint48 | num_of_sequences |
Number of sequences represented. | |
fid_Uint48 | total_length |
Total length of all sequences when concatenating them, including the sequence separators. | |
fid_Uint48constptr | descriptions |
Content of fid_Sequences::sdsfile as unsigned integers. | |
fid_Uint48constptr | separators |
Content of fid_Sequences::sspfile as unsigned integers. | |
double | distribution [UCHAR_MAX+1] |
Character distribution. | |
fid_Mappedfile | tisfile |
Sequences in binary representation. | |
fid_Mappedfile | oisfile |
Sequences in original/textual representation. | |
fid_Mappedfile | sspfile |
Sequence separators. | |
fid_Mappedfile | desfile |
Sequence descriptions. | |
fid_Mappedfile | sdsfile |
Sequence description separators. |
Integer size.
Definition at line 38 of file sequences.h.
Referenced by fid_sequences_compute_distribution(), fid_sequences_init(), and fid_sequences_realize().
const fid_Alphabet* fid_Sequences::alpha |
Reference to the alphabet the sequence data is encoded with.
Definition at line 39 of file sequences.h.
Referenced by fid_sequences_compute_distribution(), fid_sequences_init(), fid_suffixarray_compute_distribution(), and fid_suffixarray_dump().
Number of sequences represented.
Definition at line 41 of file sequences.h.
Referenced by fid_sequences_compute_distribution(), fid_sequences_index_to_boundaries(), fid_sequences_init(), fid_sequences_iterate(), fid_sequences_iterate_range(), fid_sequences_offset_to_index(), fid_sequences_parse_from_memory_to_file(), fid_suffixarray_compute_distribution(), and fid_suffixarray_dump().
Total length of all sequences when concatenating them, including the sequence separators.
Definition at line 42 of file sequences.h.
Referenced by fid_sequences_index_to_boundaries(), fid_sequences_init(), fid_sequences_iterate_range(), fid_suffixarray_dump_suffix(), fid_suffixarray_extend_interval(), fid_suffixarray_find_embedded_interval(), fid_suffixarray_find_interval(), fid_suffixarray_get_intervals(), fid_suffixarray_print(), fid_suffixinterval_find_right(), fid_suffixinterval_homepos(), and fid_suffixinterval_lcpvalue().
Content of fid_Sequences::sdsfile as unsigned integers.
Definition at line 45 of file sequences.h.
Referenced by fid_sequences_init().
Content of fid_Sequences::sspfile as unsigned integers.
Definition at line 47 of file sequences.h.
Referenced by fid_sequences_index_to_boundaries(), fid_sequences_init(), fid_sequences_iterate(), fid_sequences_iterate_range(), and fid_sequences_offset_to_index().
double fid_Sequences::distribution[UCHAR_MAX+1] |
Character distribution.
Definition at line 49 of file sequences.h.
Referenced by fid_sequences_compute_distribution(), and fid_suffixarray_compute_distribution().
Sequences in binary representation.
Definition at line 50 of file sequences.h.
Referenced by fid_create_online_files(), fid_sequences_compute_distribution(), fid_sequences_free(), fid_sequences_init(), fid_sequences_iterate_range(), fid_sequences_map(), fid_sequences_parse_from_memory_to_file(), fid_sequences_realize(), fid_suffixarray_compute_distribution(), fid_suffixarray_dump(), fid_suffixarray_dump_suffix(), fid_suffixarray_find_embedded_interval(), fid_suffixarray_get_intervals(), fid_suffixarray_suffix_length(), and fid_suffixinterval_dump().
Sequences in original/textual representation.
Definition at line 51 of file sequences.h.
Referenced by fid_create_online_files(), fid_sequences_free(), fid_sequences_init(), fid_sequences_map(), fid_sequences_parse_from_memory_to_file(), fid_sequences_realize(), and fid_suffixarray_dump().
Sequence separators.
Definition at line 53 of file sequences.h.
Referenced by fid_create_online_files(), fid_sequences_free(), fid_sequences_init(), fid_sequences_map(), fid_sequences_parse_from_memory_to_file(), and fid_suffixarray_dump().
Sequence descriptions.
Definition at line 54 of file sequences.h.
Referenced by fid_create_online_files(), fid_sequences_free(), fid_sequences_init(), fid_sequences_map(), fid_sequences_parse_from_memory_to_file(), and fid_suffixarray_dump().
Sequence description separators.
Definition at line 55 of file sequences.h.
Referenced by fid_create_online_files(), fid_sequences_free(), fid_sequences_init(), fid_sequences_map(), and fid_sequences_parse_from_memory_to_file().