Definitions used throughout BLAST.
Defines to provide correct exporting from BLAST DLL in Windows.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definitions and functions associated with the BlastQueryInfo structure.
static const char location[]
uint8_t Uint1
1-byte (8-bit) unsigned 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.
Uint1 Boolean
bool replacment for C
EPatternProgram
Options for running the pattern search.
@ eSeed
Use only those query occurrences that are specified in the input pattern file.
@ ePatMatch
Only find pattern occurrences in query, but do not search the database.
@ ePattern
Only find pattern occurrences in database, but do not perform alignments.
@ ePatSeed
Search a BLAST database using pattern occurrences as seeds.
EPatternType
Type of pattern: fits in single word, several words, or is very long.
@ eVeryLong
Is pattern too long for a simple multi-word processing?
@ eMultiWord
Does pattern consist of a multiple words?
@ eOneWord
Does pattern consist of a single word?
#define PHI_BUF_SIZE
Default size for buffers.
Int4 PHIGetPatternOccurrences(const SPHIPatternSearchBlk *pattern_blk, const BLAST_SequenceBlk *query, const BlastSeqLoc *location, Boolean is_dna, BlastQueryInfo *query_info)
Finds all pattern hits in a given query and saves them in the previously allocated SPHIQueryInfo stru...
SPHIQueryInfo * SPHIQueryInfoFree(SPHIQueryInfo *pat_info)
Frees the pattern information structure.
struct SShortPatternItems SShortPatternItems
Auxiliary items needed for a PHI BLAST search with a pattern that fits in a single word.
#define PHI_MAX_WORDS_IN_PATTERN
Maximal number of words in pattern.
#define PHI_ASCII_SIZE
Size of ASCII alphabet.
struct SDNALongPatternItems SDNALongPatternItems
Auxiliary items needed for a DNA pattern search with pattern containing multiple words.
SPHIQueryInfo * SPHIQueryInfoNew(void)
Allocates the pattern occurrences structure.
#define PHI_MAX_WORD_SIZE
Maximal word size.
Int4 FindPatternHits(Int4 *hitArray, const Uint1 *seq, Int4 len, Boolean is_dna, const SPHIPatternSearchBlk *patternSearch)
Find the places where the pattern matches seq; 3 different methods are used depending on the length o...
struct SPHIPatternSearchBlk SPHIPatternSearchBlk
Structure containing all auxiliary information needed in a pattern search.
#define PHI_MAX_PATTERN_LENGTH
Threshold pattern length.
SPHIQueryInfo * SPHIQueryInfoCopy(const SPHIQueryInfo *pat_info)
Copies the SPHIQueryInfo structure.
struct SLongPatternItems SLongPatternItems
Auxiliary items needed for a PHI BLAST search with pattern containing multiple words.
struct SExtraLongPatternItems SExtraLongPatternItems
Auxiliary items needed for a PHI BLAST search with pattern that contains pieces longer than a word.
struct SDNAShortPatternItems SDNAShortPatternItems
Structure containing auxiliary items needed for a DNA search with a pattern that fits in a single wor...
Structure to hold a sequence.
The query related information.
Used to hold a set of positions, mostly used for filtering.
Auxiliary items needed for a DNA pattern search with pattern containing multiple words.
Uint4 DNAprefixSLL[100][256]
Where prefix of DNA 4-mer matches pattern, for multiple-word patterns.
Uint4 DNAsuffixSLL[100][256]
Where suffix of DNA 4-mer matches pattern, for multiple-word patterns.
Structure containing auxiliary items needed for a DNA search with a pattern that fits in a single wor...
Uint4 * DNAwhichPrefixPosPtr
Prefix position array for DNA patterns.
Uint4 DNAwhichSuffixPositions[256]
Where suffix of DNA 4-mer matches pattern.
Uint4 * DNAwhichSuffixPosPtr
Suffix position array for DNA patterns.
Uint4 DNAwhichPrefixPositions[256]
Where prefix of DNA 4-mer matches pattern.
Auxiliary items needed for a PHI BLAST search with pattern containing multiple words.
Int4 match_maskL[100]
Bit mask representation of input pattern for long patterns.
SExtraLongPatternItems * extra_long_items
Additional items necessary if pattern contains pieces longer than a word.
SDNALongPatternItems * dna_items
Additional items necessary for a DNA pattern.
Int4 SLL[100][256]
For each letter in the alphabet and each word in the masked pattern representation,...
Int4 inputPatternMasked[(30 *11)]
Masked input pattern.
Int4 bitPatternByLetter[256][11]
Which positions can a character occur in for long patterns.
Int4 numWords
Number of words need to hold bit representation of pattern.
Structure containing all auxiliary information needed in a pattern search.
SShortPatternItems * one_word_items
Items necessary when pattern fits in one word.
EPatternType flagPatternLength
Indicates if the whole pattern fits in 1 word, each of several parts of the pattern fit in a word,...
double patternProbability
Probability of this letter combination.
Int4 minPatternMatchLength
Minimum length of string to match this pattern.
char * pattern
Pattern used, saved here for error reporting.
Int4 num_patterns_db
Number of patterns actually found during the database search.
SLongPatternItems * multi_word_items
Additional items, when pattern requires multiple words.
In PHI BLAST, structure containing information about all pattern occurrences in query.
Auxiliary items needed for a PHI BLAST search with a pattern that fits in a single word.
Int4 * whichPositionPtr
Array of positions where pattern lettern should match, for a single word of the pattern.
SDNAShortPatternItems * dna_items
Additional items for a DNA search.
Int4 match_mask
Bit mask representation of input pattern for patterns that fit in a word.
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