This data structure gathers all data required to operate on the enhanced suffix array.
Definition at line 37 of file suffixarray.h.
#include <suffixarray.h>
Data Fields | |
fid_Uintsize | uisize |
Integer size. | |
fid_Sequences | sequences |
Reference to sequence data. | |
fid_Alphabet | alpha |
The alphabet the sequence data is encoded with. | |
fid_Uint48constptr | suftab |
Plain suffix array, which is basically a correctly typed shortcut to the content of fid_Suffixarray::suffile. | |
fid_Uint48constptr | skiptab |
Skip table, basically the correctly typed content of fid_Suffixarray::skpfile. | |
fid_Uint48constptr | stitab |
Inverse suffix array, basically the correctly typed content of fid_Suffixarray::stifile. | |
fid_Uint48 | num_of_large_lcps |
The number of large lcp-values stored in file fid_Suffixarray::llvfile. | |
fid_Mappedfile | suffile |
File containing the plain suffix array. | |
fid_Mappedfile | lcpfile |
File containing the lcp-table. | |
fid_Mappedfile | llvfile |
File containing the large lcp-values. | |
fid_Mappedfile | skpfile |
File containing the skip table. | |
fid_Mappedfile | stifile |
File containing the inverse suffix array. |
Integer size.
Definition at line 39 of file suffixarray.h.
Referenced by fid_projectfile_init_from_suffixarray(), fid_suffixarray_dump(), fid_suffixarray_init(), and fid_suffixarray_realize().
Reference to sequence data.
Definition at line 40 of file suffixarray.h.
Referenced by fid_suffixarray_compute_distribution(), fid_suffixarray_dump(), fid_suffixarray_dump_suffix(), fid_suffixarray_extend_interval(), fid_suffixarray_find_embedded_interval(), fid_suffixarray_find_interval(), fid_suffixarray_free(), fid_suffixarray_get_intervals(), fid_suffixarray_init(), fid_suffixarray_load_from_files(), fid_suffixarray_print(), fid_suffixarray_realize(), fid_suffixarray_suffix_length(), fid_suffixinterval_dump(), fid_suffixinterval_find_right(), fid_suffixinterval_homepos(), and fid_suffixinterval_lcpvalue().
The alphabet the sequence data is encoded with.
Definition at line 41 of file suffixarray.h.
Referenced by fid_suffixarray_compute_distribution(), fid_suffixarray_dump(), fid_suffixarray_dump_intervals(), fid_suffixarray_dump_suffix(), fid_suffixarray_get_intervals(), fid_suffixarray_init(), fid_suffixarray_load_from_files(), fid_suffixarray_traverse(), and fid_suffixinterval_dump().
Plain suffix array, which is basically a correctly typed shortcut to the content of fid_Suffixarray::suffile.
Definition at line 43 of file suffixarray.h.
Referenced by fid_suffixarray_compute_distribution(), fid_suffixarray_dump_suffix(), fid_suffixarray_find_embedded_interval(), fid_suffixarray_get_intervals(), fid_suffixarray_init(), fid_suffixarray_print(), fid_suffixarray_suffix_length(), fid_suffixinterval_dump(), and fid_suffixinterval_lcpvalue().
Skip table, basically the correctly typed content of fid_Suffixarray::skpfile.
Definition at line 46 of file suffixarray.h.
Referenced by fid_suffixarray_init(), and fid_suffixarray_print().
Inverse suffix array, basically the correctly typed content of fid_Suffixarray::stifile.
Definition at line 48 of file suffixarray.h.
Referenced by fid_suffixarray_init(), and fid_suffixarray_print().
The number of large lcp-values stored in file fid_Suffixarray::llvfile.
Definition at line 51 of file suffixarray.h.
Referenced by fid_suffixarray_find_large_lcp(), and fid_suffixarray_init().
File containing the plain suffix array.
Definition at line 54 of file suffixarray.h.
Referenced by fid_suffixarray_dump(), fid_suffixarray_free(), fid_suffixarray_get_intervals(), and fid_suffixarray_init().
File containing the lcp-table.
Definition at line 55 of file suffixarray.h.
Referenced by fid_suffixarray_dump(), fid_suffixarray_free(), fid_suffixarray_init(), and fid_suffixinterval_homepos().
File containing the large lcp-values.
Definition at line 56 of file suffixarray.h.
Referenced by fid_suffixarray_dump(), fid_suffixarray_find_large_lcp(), fid_suffixarray_free(), and fid_suffixarray_init().
File containing the skip table.
Definition at line 57 of file suffixarray.h.
Referenced by fid_suffixarray_dump(), fid_suffixarray_free(), and fid_suffixarray_init().
File containing the inverse suffix array.
Definition at line 58 of file suffixarray.h.
Referenced by fid_suffixarray_dump(), fid_suffixarray_free(), and fid_suffixarray_init().