Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phiblast__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/unit_tests/api/phiblast_unit_test.cpp Source File

memcpy(

+1, seq.c_str(), seq.size());

(

index = 1; index <= seq.size(); ++index)

kQuerySeq(

);

x_SetupSequenceBlk(kQuerySeq, &query_blk);

BOOST_REQUIRE_EQUAL(8, gap_align->

);

BOOST_REQUIRE_EQUAL(142, gap_align->

);

BOOST_REQUIRE_EQUAL(3, esp->

);

BOOST_REQUIRE_EQUAL(45, esp->

[2]);

m_ScoreBlk.

();

kNumPatterns = 4;

{ {100,20}, {200,18}, {300,22}, {400, 21} };

kHspMax = 10;

kNumRepetitions = 4;

hsp_list->

= index;

(

hsp_index = 0; hsp_index < kHspMax; ++hsp_index) {

hsp->

= 200 - 2*index - 5*hsp_index;

(

index = 0; index < kHitlistSize; ++index) {

(index = 0; index < hitlist->

- 1; ++index) {

kNumHspLists = 20;

(

hitlist_index = 0; hitlist_index < num_results;

BOOST_REQUIRE(results_array[hitlist_index] !=

);

BOOST_REQUIRE(x_CheckIncreasingBestEvalues(hitlist));

kHspCnt = (13-hitlist_index)/num_results;

(

hsplist_index = 0; hsplist_index < kNumHspLists;

BOOST_REQUIRE_EQUAL(kHspCnt, hsplist->

);

BOOST_REQUIRE_EQUAL(hsplist_index, hsplist->

);

(

hsp_index = 0; hsp_index < kHspCnt; ++hsp_index) {

BOOST_REQUIRE_EQUAL(hitlist_index,

results_array[hitlist_index] =

(results_array);

setUpLookupTable(

);

BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std);

BOOST_REQUIRE(m_ScoreBlk->kbp == m_ScoreBlk->kbp_std);

BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC);

BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0);

BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->Lambda,

m_ScoreBlk->kbp_gap[0]->Lambda);

BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K);

setUpLookupTable(

);

BOOST_REQUIRE(m_ScoreBlk->kbp_gap == m_ScoreBlk->kbp_gap_std);

BOOST_REQUIRE(m_ScoreBlk->kbp == m_ScoreBlk->kbp_std);

BOOST_REQUIRE_EQUAL(0.5, m_ScoreBlk->kbp_gap[0]->paramC);

BOOST_REQUIRE(m_ScoreBlk->kbp_gap[0]->H != 0);

BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->Lambda,

m_ScoreBlk->kbp_gap[0]->Lambda);

BOOST_REQUIRE_EQUAL(m_ScoreBlk->kbp[0]->K, m_ScoreBlk->kbp_gap[0]->K);

setUpLookupTable(

);

x_FindQueryOccurrences();

BOOST_REQUIRE_CLOSE(0.0013,

->probability, 1);

BOOST_REQUIRE_EQUAL(37, m_QueryInfo->contexts[0].length_adjustment);

setUpLookupTable(

);

x_FindQueryOccurrences();

BOOST_REQUIRE_CLOSE(0.000262,

->probability, 1);

BOOST_REQUIRE_EQUAL(3, m_QueryInfo->contexts[0].length_adjustment);

kNumDbHits = 33;

setUpLookupTable(

);

x_FindQueryOccurrences();

BOOST_REQUIRE_CLOSE(7.568e-59, hsp->

, 1);

BOOST_REQUIRE(hsp_list ==

);

setUpLookupTable(

);

kSubjectSeq(

);

kNumHits = 3;

kStarts[kNumHits] = { 8, 11, 94 };

kEnds[kNumHits] = { 52, 52, 133 };

start_offset = 0;

x_SetupSequenceBlk(kSubjectSeq, &subject_blk);

BOOST_REQUIRE_EQUAL(kNumHits, hit_count);

(

index = 0; index < kNumHits; ++index) {

BOOST_REQUIRE_EQUAL(kStarts[index],

(

) offset_pairs[index].phi_offsets.

);

BOOST_REQUIRE_EQUAL(kEnds[index],

(

) offset_pairs[index].phi_offsets.

);

(offset_pairs);

setUpLookupTable(

);

kQuerySeq(

);

kSubjectSeq(

);

kQueryPatLength = 40;

kQueryStart = 94;

x_SetupSequenceBlk(kQuerySeq, &query_blk);

x_SetupSequenceBlk(kSubjectSeq, &subject_blk);

kSubjectPatLength = 45;

kSubjectStart = 8;

m_QueryInfo, &ext_params);

subject_blk->

, m_ScoreBlk,

score_params, kQueryStart, kSubjectStart,

kQueryPatLength, kSubjectPatLength,

x_CheckGappedAlignmentResults(gap_align);

setUpLookupTable(

);

x_CheckSplitResults(results_array,

->num_patterns);

setUpLookupTable(

);

BOOST_REQUIRE(results_array !=

);

BOOST_REQUIRE(results_array[0] ==

);

(results_array);

kIsGapped =

;

setUpLookupTable(

);

x_FindQueryOccurrences();

m_QueryInfo->contexts[0].eff_searchsp = 10000000;

k_avg_subject_length=343;

BOOST_REQUIRE(ext_options ==

);

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(hit_options ==

);

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

union BlastOffsetPair BlastOffsetPair

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...

#define sfree(x)

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

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

BlastSeqLoc * BlastSeqLocNew(BlastSeqLoc **head, Int4 from, Int4 to)

Create and initialize a new sequence interval.

Int2 BLAST_GapAlignStructNew(const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, Uint4 max_subject_length, BlastScoreBlk *sbp, BlastGapAlignStruct **gap_align_ptr)

Initializes the BlastGapAlignStruct structure.

BlastHSP * Blast_HSPNew(void)

Allocate and zeros out memory for an HSP structure.

BlastHSPResults * Blast_HSPResultsFree(BlastHSPResults *results)

Deallocate memory for BLAST results.

void Blast_HSPListPHIGetEvalues(BlastHSPList *hsp_list, BlastScoreBlk *sbp, const BlastQueryInfo *query_info, const SPHIPatternSearchBlk *pattern_blk)

Calculate e-values for a PHI BLAST HSP list.

Int2 Blast_HSPResultsInsertHSPList(BlastHSPResults *results, BlastHSPList *hsp_list, Int4 hitlist_size)

Blast_HSPResultsInsertHSPList Insert an HSP list to the appropriate place in the results structure.

BlastHSPList * Blast_HSPListNew(Int4 hsp_max)

Creates HSP list structure with a default size HSP array.

BlastHSPResults * Blast_HSPResultsNew(Int4 num_queries)

Initialize the results structure.

Boolean Blast_HSPListIsSortedByScore(const BlastHSPList *hsp_list)

Check if HSP list is sorted by score.

Int2 Blast_HSPListSaveHSP(BlastHSPList *hsp_list, BlastHSP *hsp)

Saves HSP information into a BlastHSPList structure.

BlastHSPResults ** PHIBlast_HSPResultsSplit(const BlastHSPResults *results, const SPHIQueryInfo *pattern_info)

Splits the BlastHSPResults structure for a PHI BLAST search into an array of BlastHSPResults structur...

BlastHSPList * Blast_HSPListFree(BlastHSPList *hsp_list)

Deallocate memory for an HSP list structure as well as all it's components.

BlastHitSavingOptions * BlastHitSavingOptionsFree(BlastHitSavingOptions *options)

Deallocate memory for BlastHitSavingOptions.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

Int2 LookupTableOptionsNew(EBlastProgramType program, LookupTableOptions **options)

Allocate memory for lookup table options and fill with default values.

BlastExtensionOptions * BlastExtensionOptionsFree(BlastExtensionOptions *options)

Deallocate memory for BlastExtensionOptions.

Int2 BlastHitSavingOptionsNew(EBlastProgramType program, BlastHitSavingOptions **options, Boolean gapped_calculation)

Allocate memory for BlastHitSavingOptions.

Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)

Allocate memory for BlastExtensionOptions and fill with default values.

BlastHitSavingParameters * BlastHitSavingParametersFree(BlastHitSavingParameters *parameters)

Deallocate memory for BlastHitSavingOptions*.

Int2 BlastExtensionParametersNew(EBlastProgramType blast_program, const BlastExtensionOptions *options, BlastScoreBlk *sbp, BlastQueryInfo *query_info, BlastExtensionParameters **parameters)

Calculate the raw values for the X-dropoff parameters.

Int2 BlastScoringParametersNew(const BlastScoringOptions *options, BlastScoreBlk *sbp, BlastScoringParameters **parameters)

Calculate scaled cutoff scores and gap penalties.

Int2 BlastHitSavingParametersNew(EBlastProgramType program_number, const BlastHitSavingOptions *options, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters **parameters)

Allocate memory and initialize the BlastHitSavingParameters structure.

EBlastProgramType

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

BlastQueryInfo * BlastQueryInfoNew(EBlastProgramType program, int num_queries)

Allocate memory for query information structure.

Utilities initialize/setup BLAST.

Int2 BlastSetup_ScoreBlkInit(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastScoringOptions *scoring_options, EBlastProgramType program_number, BlastScoreBlk **sbpp, double scale_factor, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

Initializes the score block structure.

Int2 Blast_SetPHIPatternInfo(EBlastProgramType program, const SPHIPatternSearchBlk *pattern_blk, const BLAST_SequenceBlk *query, const BlastSeqLoc *lookup_segments, BlastQueryInfo *query_info, Blast_Message **blast_message)

In a PHI BLAST search, adds pattern information to the BlastQueryInfo structure.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

Int2 BlastSeqBlkSetSequence(BLAST_SequenceBlk *seq_blk, const Uint1 *sequence, Int4 seqlen)

Stores the sequence in the sequence block structure.

Int2 BlastSeqBlkNew(BLAST_SequenceBlk **retval)

Allocates a new sequence block structure.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

Wrapper class for BLAST_SequenceBlk .

Wrapper class for BlastExtensionOptions .

Wrapper class for BlastExtensionParameters .

Wrapper class for BlastGapAlignStruct .

Wrapper class for BlastQueryInfo .

Wrapper class for BlastScoreBlk .

Wrapper class for BlastScoringOptions .

Wrapper class for BlastScoringParameters .

Wrapper class for Blast_Message .

Wrapper class for LookupTableOptions .

Wrapper class for LookupTableWrap .

static bool x_CheckIncreasingBestEvalues(BlastHitList *hitlist)

void x_SetupSequenceBlk(const string &seq, BLAST_SequenceBlk **seq_blk)

EBlastProgramType m_Program

CBlastQueryInfo m_QueryInfo

CBlastScoreBlk m_ScoreBlk

static BlastHSPList * x_SetupHSPList(int index)

CPhiblastTestFixture()

Set up: initializes the PHI "lookup table", aka the SPHIPatternSearchBlk structure,...

void setUpLookupTable(string pattern)

void x_FindQueryOccurrences(void)

After the initial set-up is done, finds pattern occurrences in query and fills the pattern informatio...

static SPHIQueryInfo * x_SetupPatternInfo(void)

static void x_CheckSplitResults(BlastHSPResults **results_array, int num_results)

void x_CheckGappedAlignmentResults(BlastGapAlignStruct *gap_align)

static BlastHSPResults * x_SetupResults(const int kHitlistSize)

CLookupTableWrap m_Lookup

Ensure direct dependencies on enough of the core xncbi library to satisfy shared libraries that depen...

static const char location[]

void Reset(LookupTableWrap *p=NULL)

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

void Reset(BlastScoreBlk *p=NULL)

void Reset(BlastQueryInfo *p=NULL)

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

Wrapper for all lookup tables used in BLAST.

Int4 GetOffsetArraySize(LookupTableWrap *lookup)

Determine the size of the offsets arrays to be filled by the ScanSubject function.

Int2 LookupTableWrapInit(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc)

Create the lookup table for all query words.

#define TRUE

bool replacment for C indicating true.

@ eVeryLong

Is pattern too long for a simple multi-word processing?

@ eOneWord

Does pattern consist of a single word?

SPHIQueryInfo * SPHIQueryInfoFree(SPHIQueryInfo *pat_info)

Frees the pattern information structure.

SPHIQueryInfo * SPHIQueryInfoNew(void)

Allocates the pattern occurrences structure.

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

Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback.

Int2 PHIGappedAlignmentWithTraceback(Uint1 *query, Uint1 *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length, Int4 q_pat_length, Int4 s_pat_length, SPHIPatternSearchBlk *pattern_blk)

Perform a gapped alignment with traceback for PHI BLAST.

Pseudo lookup table structure and database scanning functions used in PHI-BLAST.

Int4 PHIBlastScanSubject(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *query_blk, const BLAST_SequenceBlk *subject, Int4 *offset, BlastOffsetPair *offset_pairs, Int4 array_size)

Scans the subject sequence from "offset" to the end of the sequence.

BOOST_AUTO_TEST_CASE(testPHILookupTableLong)

Tests the values in the PHI BLAST lookup table.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure to hold a sequence.

Int4 length

Length of sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Options used for gapped extension These include: a.

Structure supporting the gapped alignment.

Int4 query_stop

query end offseet of current alignment

Int4 subject_start

subject start offset current alignment

Int4 query_start

query start offset of current alignment

Int4 subject_stop

subject end offset of current alignment

Int4 score

Return value: alignment score.

GapEditScript * edit_script

The traceback (gap) information.

Int4 cutoff_score

Raw cutoff score corresponding to the e-value provided by the user if no sum stats,...

The structure to hold all HSPs for a given sequence after the gapped alignment.

Int4 oid

The ordinal id of the subject sequence this HSP list is for.

Int4 hspcnt

Number of HSPs saved.

BlastHSP ** hsp_array

Array of pointers to individual HSPs.

double best_evalue

Smallest e-value for HSPs in this list.

The structure to contain all BLAST results, for multiple queries.

BlastHitList ** hitlist_array

Array of results for individual query sequences.

Structure holding all information about an HSP.

SPHIHspInfo * pat_info

In PHI BLAST, information about this pattern match.

double evalue

This HSP's e-value.

Int4 score

This HSP's raw score.

The structure to contain all BLAST results for one query sequence.

BlastHSPList ** hsplist_array

Array of HSP lists for individual database hits.

Int4 hsplist_count

Filled size of the HSP lists array.

Options used when evaluating and saving hits These include: a.

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

BlastGappedCutoffs * cutoffs

per-context gapped cutoff information

Int4 cutoff_score_min

smallest cutoff score across all contexts

Boolean gapped_calculation

gap-free search if FALSE

Used to hold a set of positions, mostly used for filtering.

Edit script: linked list of correspondencies between two sequences.

Int4 * num

Array of number of operations.

Int4 size

Size of above arrays.

char * phi_pattern

PHI-BLAST pattern.

void * lut

Pointer to the actual lookup table structure.

SExtraLongPatternItems * extra_long_items

Additional items necessary if pattern contains pieces longer than a word.

Int4 numWords

Number of words need to hold bit representation of pattern.

In PHI BLAST: information about pattern match in a given HSP.

Int4 index

Index of query pattern occurrence for this HSP.

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,...

double patternProbability

Probability of this letter combination.

Int4 minPatternMatchLength

Minimum length of string to match this pattern.

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.

Int4 allocated_size

Allocated size of the occurrences array.

Int4 num_patterns

Number of pattern occurrences in query.

SPHIPatternInfo * occurrences

Array of pattern occurrence information structures.

Int4 * whichPositionPtr

Array of positions where pattern lettern should match, for a single word of the pattern.

Int4 match_mask

Bit mask representation of input pattern for patterns that fit in a word.

Utility stuff for more convenient using of Boost.Test library.

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 s_end

End offset of pattern in subject.

voidp calloc(uInt items, uInt size)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4