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NCBI C++ ToolKit: src/algo/blast/core/pattern.c Source File

kCheckingMatches = s &

;

((kCheckingMatches >> right_index) % 2 == 1)

((

>> right_index) %2 == 1)

left_index = right_index;

*rightOne = right_index;

*rightMaskOnly = left_index;

(rightOne - rightMaskOnly);

prefixMatchedBitPattern = 0;

maskShiftPlus1 = (

<< 1) + 1;

(

= 0;

< len1;

++) {

prefixMatchedBitPattern =

((prefixMatchedBitPattern << 1) | maskShiftPlus1) &

(prefixMatchedBitPattern &

) {

hitArray[numMatches++] =

;

hitArray[numMatches++] =

-

(prefixMatchedBitPattern,

)+1;

prefixMatchedBitPattern;

twiceNumHits = 0;

kMaskShiftPlus1 = (kMatchMask << 1)+1;

prefixMatchedBitPattern =

((kMatchMask * ((1 << (pos+1))-1)*2) + (1 << (pos+1))-1) &

remain = (

-pos) % 4;

prefixMatchedBitPattern = kMaskShiftPlus1;

(

= 0;

< end;

++) {

( (

= (prefixMatchedBitPattern &

(j = 0; j < 4; j++) {

(

& kMatchMask) {

hitArray[twiceNumHits++] =

*4 + j + pos;

hitArray[twiceNumHits++] =

*4 + j + pos -

prefixMatchedBitPattern =

(((prefixMatchedBitPattern << 4) | kMask2) &

( (

= (prefixMatchedBitPattern &

(j = 0; j < remain; j++) {

(

& kMatchMask) {

hitArray[twiceNumHits++] =

*4+j + pos;

hitArray[twiceNumHits++] =

*4+j + pos -

(

= 0;

< numWords;

++) {

x = (

[

] << 1) +

;

(x >= kOverflowThreshold) {

[

] = x - kOverflowThreshold;

(

= 0;

< numWords;

++)

[

] = (

[

] |

[

]);

returnValue = 0;

(

= 0;

< numWords;

++) {

(wordIndex = 0; wordIndex < numWords; wordIndex++) {

((s[wordIndex] >> bitIndex) % 2 == 1)

((

[wordIndex] >> bitIndex) %2 == 1)

*prefixMatchedBitPattern;

twiceNumHits = 0;

prefixMatchedBitPattern = (

*)

(num_words,

(

));

(wordIndex = 0; wordIndex < num_words; wordIndex++) {

prefixMatchedBitPattern[wordIndex] = 0;

(

= 0;

< len1;

++) {

hitArray[twiceNumHits++] =

;

hitArray[twiceNumHits++] =

-

(prefixMatchedBitPattern);

twiceHitsOneCall;

nextPosInHitArray;

hitIndex1, hitIndex2;

(twiceNumHits < 2)

(wordIndex = most_specific_word+1;

wordIndex < multiword_items->

; wordIndex++) {

nextPosInHitArray = 0;

(hitIndex2 = 0; hitIndex2 < twiceNumHits; hitIndex2 += 2) {

hitArray[hitIndex2]+1,

(

-hitArray[hitIndex2]-1,

extra_items->

[wordIndex-1] +

is_dna, pattern_blk);

(hitIndex1 = 0; hitIndex1 < twiceHitsOneCall; hitIndex1+= 2) {

hitArray1[nextPosInHitArray+hitIndex1] =

hitArray[hitIndex2]+hitArray1[nextPosInHitArray+hitIndex1]+1;

hitArray1[nextPosInHitArray+hitIndex1+1] = hitArray[hitIndex2+1];

nextPosInHitArray += twiceHitsOneCall;

twiceNumHits = nextPosInHitArray;

(twiceNumHits < 2)

(hitIndex2 = 0; hitIndex2 < nextPosInHitArray; hitIndex2++)

hitArray[hitIndex2] = hitArray1[hitIndex2];

(wordIndex = most_specific_word-1; wordIndex >=0;

nextPosInHitArray = 0;

(hitIndex2 = 0; hitIndex2 < twiceNumHits; hitIndex2 += 2) {

start = hitArray[hitIndex2+1] - extra_items->

[wordIndex] -

hitArray[hitIndex2+1]-start, is_dna, pattern_blk);

(hitIndex1 = 0; hitIndex1 < twiceHitsOneCall; hitIndex1+= 2) {

hitArray1[nextPosInHitArray+hitIndex1] = hitArray[hitIndex2];

hitArray1[nextPosInHitArray+hitIndex1+1] = start +

hitArray1[nextPosInHitArray+hitIndex1+1];

nextPosInHitArray += twiceHitsOneCall;

twiceNumHits = nextPosInHitArray;

(twiceNumHits < 2)

(hitIndex2 = 0; hitIndex2 < nextPosInHitArray; hitIndex2++)

hitArray[hitIndex2] = hitArray1[hitIndex2];

kMinPhiLookupSize = 8;

, twiceNumHits;

loc_length = to - from + 1;

sequence =

->sequence + from;

twiceNumHits =

(hitArray, sequence, loc_length, is_dna,

(

= 0;

< twiceNumHits;

+= 2) {

(hitArray[

+1]+from == 0 &&

hitArray[

]-hitArray[

+1]+1);

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Int4 BlastQueryInfoGetQueryLength(const BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index)

Obtains the sequence length for a given query in the query, without taking into consideration any app...

ncbi::TMaskedQueryRegions mask

static const char location[]

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

#define MIN(a, b)

returns smaller of a and b.

#define INT4_MAX

largest nubmer represented by signed int

void * BlastMemDup(const void *orig, size_t size)

Copies memory using memcpy and malloc.

Uint1 Boolean

bool replacment for C

#define ASSERT

macro for assert.

static Int4 s_FindHitsShortDNA(Int4 *hitArray, const Uint1 *seq, Int4 pos, Int4 len, const SPHIPatternSearchBlk *pattern_blk)

Find hits when sequence is DNA and pattern is short returns twice the number of hits.

static Int4 s_LenOfL(Int4 *s, Int4 *mask, Int4 numWords)

Returns the difference between the offset F of a first 1-bit in a word sequence and the first offset ...

static Int4 s_FindHitsVeryLong(Int4 *hitArray, const Uint1 *seq, Int4 len, Boolean is_dna, const SPHIPatternSearchBlk *pattern_blk)

Find matches when pattern is very long,.

static Int4 s_LenOf(Int4 s, Int4 mask)

Looks for 1 bits in the same position of s and mask Let R be the rightmost position where s and mask ...

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...

Int4 _PHIBlastFindHitsShort(Int4 *hitArray, const Uint1 *seq, Int4 len1, const SPHIPatternSearchBlk *pattern_blk)

Routine to find hits of pattern to sequence when sequence is proteins.

SPHIQueryInfo * SPHIQueryInfoFree(SPHIQueryInfo *pat_info)

Frees the pattern information structure.

Int4 FindPatternHits(Int4 *hitArray, const Uint1 *seq, Int4 len, Boolean is_dna, const SPHIPatternSearchBlk *pattern_blk)

Find the places where the pattern matches seq; 3 different methods are used depending on the length o...

void _PHIPatternWordsLeftShift(Int4 *a, Uint1 b, Int4 numWords)

Shift each word in the array left by 1 bit and add bit b.

static Int2 s_PHIBlastAddPatternHit(SPHIQueryInfo *pattern_info, Int4 offset, Int4 length)

Adds a new pattern hit to the PHI BLAST pseudo lookup table.

Int4 _PHIPatternWordsBitwiseAnd(Int4 *result, Int4 *a, Int4 *b, Int4 numWords)

Do a word-by-word bit-wise and of two integer arrays and put the result in a new array.

static Int4 s_FindHitsShortHead(Int4 *hitArray, const Uint1 *seq, Int4 start, Int4 len, Uint1 is_dna, const SPHIPatternSearchBlk *pattern_blk)

Top level routine to find hits when pattern has a short description.

void _PHIGetRightOneBits(Int4 s, Int4 mask, Int4 *rightOne, Int4 *rightMaskOnly)

Looks for 1 bits in the same position of s and mask Let R be the rightmost position where s and mask ...

static Int4 s_FindHitsLong(Int4 *hitArray, const Uint1 *seq, Int4 len1, const SPHIPatternSearchBlk *pattern_blk)

Finds places where pattern matches seq and returns them as pairs of positions in consecutive entries ...

void _PHIPatternWordsBitwiseOr(Int4 *a, Int4 *b, Int4 numWords)

Do a word-by-word bit-wise or of two integer arrays and put the result back in the first array.

SPHIQueryInfo * SPHIQueryInfoCopy(const SPHIQueryInfo *pat_info)

Copies the SPHIQueryInfo structure.

SPHIQueryInfo * SPHIQueryInfoNew()

Allocates the pattern occurrences structure.

Functions for finding pattern matches in sequence (PHI-BLAST).

@ eMultiWord

Does pattern consist of a multiple words?

@ eOneWord

Does pattern consist of a single word?

#define PHI_BITS_PACKED_PER_WORD

Number of bits packed in a word.

#define PHI_MAX_HIT

Maximal size of an array of pattern hits.

Auxiliary functions for finding pattern matches in sequence (PHI-BLAST), that are used in multiple so...

static int pattern_info(int what, void *where, BOOL unsetok)

Structure to hold a sequence.

The query related information.

struct SPHIQueryInfo * pattern_info

Counts of PHI BLAST pattern occurrences, used in PHI BLAST only.

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

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.

Uint4 * DNAwhichPrefixPosPtr

Prefix position array for DNA patterns.

Uint4 * DNAwhichSuffixPosPtr

Suffix position array for DNA patterns.

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 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.

Information about a single pattern occurence in the query.

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,...

SLongPatternItems * multi_word_items

Additional items, when pattern requires multiple words.

In PHI BLAST, structure containing information about all pattern occurrences in query.

char * pattern

Pattern used, saved here for formatting purposes.

Int4 num_patterns

Number of pattern occurrences in query.

SPHIPatternInfo * occurrences

Array of pattern occurrence information structures.

Int4 left

left endpoint of range (zero based)

Int4 right

right endpoint of range (zero based)

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.

voidp calloc(uInt items, uInt size)

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