fid_Sequences Struct Reference
[Binary encoded multiple sequences]

A structure that holds references to persistent suffix array tables. More...


Detailed Description

A structure that holds references to persistent suffix array tables.

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>

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Data Fields

fid_Uintsize uisize
 Integer size.
const fid_Alphabetalpha
 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.

Field Documentation

Integer size.

Definition at line 38 of file sequences.h.

Referenced by fid_sequences_compute_distribution(), fid_sequences_init(), and fid_sequences_realize().

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().

Content of fid_Sequences::sdsfile as unsigned integers.

Definition at line 45 of file sequences.h.

Referenced by fid_sequences_init().

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().

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().


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