( (
b->right <
a->left) || (
b->left >
a->right) )
union BlastOffsetPair BlastOffsetPair
This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...
struct SPHIPatternInfo SPHIPatternInfo
Information about a single pattern occurence in the query.
struct SBlastProgress SBlastProgress
Progress monitoring structure.
ESubjectMaskingType
Define the possible subject masking types.
void SBlastProgressReset(SBlastProgress *progress_info)
Resets the progress structure to its original state (as if newly allocated) for a fresh start without...
struct SPHIQueryInfo SPHIQueryInfo
In PHI BLAST, structure containing information about all pattern occurrences in query.
Int4 SSeqRangeArrayLessThanOrEqual(const SSeqRange *ranges, Int4 num_ranges, Int4 target)
Returns the index of the range, such that this element is the first range that either contains the ta...
const double kSegLocut
Locut parameter for SEG.
SBlastProgress * SBlastProgressNew(void *user_data)
Allocates and initializes a new SBlastProgress structure.
SSeqRange SSeqRangeNew(Int4 start, Int4 stop)
Create a new SSeqRange structure with both fields initialized.
Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)
Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...
SBlastProgress * SBlastProgressFree(SBlastProgress *progress_info)
Deallocates a SBlastProgress structure.
const int kDustLinker
Parameter used by dust to link together close low-complexity segments.
const int kSegWindow
Window that SEG examines at once.
struct SSeqRange SSeqRange
A structure containing two integers, used e.g.
struct BlastSeqLoc BlastSeqLoc
Used to hold a set of positions, mostly used for filtering.
static NCBI_INLINE Boolean SSeqRangeIntersectsWith(const SSeqRange *a, const SSeqRange *b)
Determine if two ranges intersect.
struct SBlastTargetTranslation SBlastTargetTranslation
Information about target translations.
struct BlastMaskLoc BlastMaskLoc
Structure for keeping the query masking information.
const double kSegHicut
Hicut parameter for SEG.
const int kDustLevel
Level parameter used by dust.
struct BLAST_SequenceBlk BLAST_SequenceBlk
Structure to hold a sequence.
const int kDustWindow
Window parameter used by dust.
const int kUngappedHSPNumMax
Maximum number of HPSs to be saved in an ungapped search.
EBlastStage
Enumeration for the stages in the BLAST search.
@ eBoth
Both preliminary and traceback stages.
@ eTracebackSearch
Traceback stage.
@ ePrelimSearch
Preliminary stage.
void __sfree(void **x)
Implemented in blast_util.c.
Defines to provide correct exporting from BLAST DLL in Windows.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definitions for various programs supported by core BLAST.
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
uint8_t Uint1
1-byte (8-bit) unsigned integer
int16_t Int2
2-byte (16-bit) signed integer
int32_t Int4
4-byte (32-bit) signed integer
uint32_t Uint4
4-byte (32-bit) unsigned integer
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
#define NCBI_INLINE
"inline" seems to work on our remaining in-house compilers (WorkShop, Compaq, ICC,...
Uint1 Boolean
bool replacment for C
#define TRUE
bool replacment for C indicating true.
#define FALSE
bool replacment for C indicating false.
Structure to hold a sequence.
Uint1 * sequence_start
Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte.
Int4 oid
The ordinal id of the current sequence.
Uint1 * compressed_nuc_seq_start
start of compressed_nuc_seq
Uint4 num_seq_ranges
Number of elements in seq_ranges.
Boolean sequence_allocated
TRUE if memory has been allocated for sequence.
BlastMaskLoc * lcase_mask
Locations to be masked from operations on this sequence: lookup table for query; scanning for subject...
SSeqRange * seq_ranges
Ranges of the sequence to search.
Boolean lcase_mask_allocated
TRUE if memory has been allocated for lcase_mask.
Int4 length
Length of sequence.
ESubjectMaskingType mask_type
type of subject masking
Int2 frame
Frame of the query, needed for translated searches.
Uint1 * sequence_nomask
Start of query sequence without masking.
Boolean seq_ranges_allocated
TRUE if memory has been allocated for seq_ranges.
Uint1 * sequence_start_nomask
Query sequence without masking.
Uint1 * sequence
Sequence used for search (could be translation).
Int2 subject_strand
Strand of the subject sequence for translated searches.
Boolean oof_sequence_allocated
TRUE if memory has been allocated for oof_sequence.
Boolean nomask_allocated
If false the two above are just pointers to sequence and sequence_start.
Int4 chunk
Used for indexing only: the chunk number within the subject sequence.
Uint1 * compressed_nuc_seq
4-to-1 compressed version of sequence
Boolean sequence_start_allocated
TRUE if memory has been allocated for sequence_start.
Uint1 * oof_sequence
Mixed-frame protein representation of a nucleotide sequence for out-of-frame alignment.
Uint1 * gen_code_string
for nucleotide subject sequences (tblast[nx]), the genetic code used to create a translated protein s...
Structure for keeping the query masking information.
Int4 total_size
Total size of the BlastSeqLoc array below.
BlastSeqLoc ** seqloc_array
Array of masked locations.
Used to hold a set of positions, mostly used for filtering.
SSeqRange * ssr
location data on the sequence.
struct BlastSeqLoc * next
next in linked list
Progress monitoring structure.
EBlastStage stage
Stage of the BLAST search currently in progress.
void * user_data
Pointer to user-provided data.
Information about target translations.
EBlastProgramType program_number
Program being run.
Int4 * range
start and stop of translated sequences.
Int4 num_frames
how many frames, one dimension of translation_buffer.
const Uint1 * gen_code_string
Genetic code string for translation.
BLAST_SequenceBlk * subject_blk
target sequence being translated.
Uint1 ** translations
two dimensional array for translations.
Boolean partial
specifies that nucleotide sequence is too long to translated.
Information about a single pattern occurence in the query.
Int4 length
Length of this pattern occurrence.
Int4 offset
Starting offset of this pattern occurrence.
In PHI BLAST, structure containing information about all pattern occurrences in query.
char * pattern
Pattern used, saved here for formatting purposes.
Int4 allocated_size
Allocated size of the occurrences array.
double probability
Estimated probability of the pattern.
Int4 num_patterns
Number of pattern occurrences in query.
SPHIPatternInfo * occurrences
Array of pattern occurrence information structures.
A structure containing two integers, used e.g.
Int4 left
left endpoint of range (zero based)
Int4 right
right endpoint of range (zero based)
This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...
Uint4 s_start
Start offset of pattern in subject.
Uint4 q_off
Query offset.
Uint4 s_off
Subject offset.
struct BlastOffsetPair::@6 qs_offsets
Query/subject offset pair.
Uint4 s_end
End offset of pattern in subject.
struct BlastOffsetPair::@7 phi_offsets
Pattern offsets in subject (PHI BLAST only)
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