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

;

kGi_130912_Length = 253;

kGi_130912_[kGi_130912_Length] = {

12, 1, 13, 11, 7, 3, 20, 12, 11, 19, 11, 6, 19, 1, 18,

20, 17, 4, 11, 7, 11, 3, 10, 10, 16, 14, 10, 14, 7, 7,

20, 13, 18, 7, 7, 17, 16, 22, 14, 7, 15, 7, 17, 14, 7,

7, 13, 16, 22, 14, 14, 15, 7, 7, 7, 7, 20, 7, 15, 14,

8, 7, 7, 7, 20, 7, 15, 14, 8, 7, 7, 7, 20, 7, 15,

14, 8, 7, 7, 7, 20, 7, 15, 14, 8, 7, 7, 7, 20, 7,

15, 7, 7, 7, 18, 8, 17, 15, 20, 13, 10, 14, 17, 10, 14,

10, 18, 13, 12, 10, 8, 12, 1, 7, 1, 1, 1, 1, 7, 1,

19, 19, 7, 7, 11, 7, 7, 22, 12, 11, 7, 17, 1, 12, 17,

16, 14, 9, 9, 8, 6, 7, 17, 4, 22, 5, 4, 16, 22, 22,

16, 5, 13, 12, 8, 16, 22, 14, 13, 15, 19, 22, 22, 16, 14,

12, 4, 5, 22, 17, 13, 15, 13, 13, 6, 19, 8, 4, 3, 19,

13, 9, 18, 9, 10, 15, 8, 18, 19, 18, 18, 18, 18, 10, 7,

5, 13, 6, 18, 5, 18, 4, 19, 10, 12, 12, 5, 16, 19, 19,

5, 15, 12, 3, 9, 18, 15, 22, 5, 16, 5, 17, 15, 1, 22,

22, 15, 16, 7, 17, 17, 12, 19, 11, 6, 17, 17, 14, 14, 19,

9, 11, 11, 9, 17, 6, 11, 9, 6, 11, 9, 19, 7};

BOOST_REQUIRE_EQUAL((

)kGi_130912_Length, seq_blk->

);

(

= 0;

< seq_blk->

;

++) {

os << prefix <<

<<

<< endl;

BOOST_REQUIRE_MESSAGE((

)seq_blk->

[

] == (

)kGi_130912_[

],

BOOST_REQUIRE_EQUAL(1,

BOOST_REQUIRE_EQUAL(1,

vector<EBlastProgramType> programs =

(vector<EBlastProgramType>, program, programs) {

BOOST_REQUIRE_MESSAGE(reference ==

,

+

);

vector<EBlastProgramType> programs =

(vector<EBlastProgramType>, program, programs) {

BOOST_REQUIRE_MESSAGE(reference ==

,

+

);

vector<EBlastProgramType> programs =

(vector<EBlastProgramType>, program, programs) {

BOOST_REQUIRE_MESSAGE(reference ==

,

+

);

vector<EBlastProgramType> programs =

(vector<EBlastProgramType>, program, programs) {

BOOST_REQUIRE_MESSAGE(reference ==

,

+

);

vector<EBlastProgramType> programs =

(vector<EBlastProgramType>, program, programs) {

BOOST_REQUIRE_MESSAGE(reference ==

,

+

);

.reserve(programs.size());

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

BOOST_REQUIRE_EQUAL(programs.size(),

.size());

(

= 0;

< programs.size();

++) {

BOOST_REQUIRE((matrix_path !=

) && (strlen(matrix_path) > 0));

ignoreFile(

);

BOOST_REQUIRE(matrix_path ==

);

ignoreFile(

.get());

BOOST_REQUIRE((matrix_path !=

) && (strlen(matrix_path) > 0));

BOOST_REQUIRE(matrix_path ==

);

BOOST_REQUIRE(matrix_path ==

);

kNumPrograms = 4;

* program_strings[kNumPrograms] = {

error_prefix(

);

(

= 0;

< kNumPrograms;

++) {

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)0,

error_prefix + program_strings[

]);

(

);

BOOST_REQUIRE_MESSAGE((

)frame == (

)1,

);

BOOST_REQUIRE_MESSAGE((

)frame == (

)-1,

);

BOOST_REQUIRE_MESSAGE((

)frame == (

)-1,

);

BOOST_REQUIRE_MESSAGE((

)frame == (

)1,

);

kNumPrograms = 3;

* program_strings[kNumPrograms] = {

error_prefix(

);

(

= 0;

< kNumPrograms;

++) {

BOOST_REQUIRE_MESSAGE((

)frame == (

)-1,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)-2,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)-3,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)1,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)2,

error_prefix + program_strings[

]);

BOOST_REQUIRE_MESSAGE((

)frame == (

)3,

error_prefix + program_strings[

]);

BOOST_REQUIRE_EQUAL((

)127, (

)frame);

BOOST_REQUIRE_EQUAL((

)127, (

)frame);

seqloc_v.push_back(*sseqloc);

unique_ptr<CBlastOptionsHandle>

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

(seqloc_v, opts_handle->GetOptions().GetProgramType(),

BOOST_REQUIRE(maxlen != 0);

BOOST_REQUIRE(seqlen != 0);

BOOST_REQUIRE(seqblk_v.size() == (

)1);

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

BOOST_REQUIRE((*itr)->lcase_mask ==

);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

pair<TSeqPos, TSeqPos> range(50, 157);

unique_ptr<SSeqLoc> sseqloc(

seqloc_v.push_back(*sseqloc);

unique_ptr<CBlastOptionsHandle>

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

(seqloc_v, opts_handle->GetOptions().GetProgramType(),

seqlen = range.second - range.first + 1;

BOOST_REQUIRE(maxlen != 0);

BOOST_REQUIRE(seqlen != 0);

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

BOOST_REQUIRE(seqblk_v.size() == (

)1);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

BOOST_REQUIRE((*itr)->lcase_mask ==

);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, kRange,

));

BOOST_REQUIRE(seqloc_v.begin()->mask.NotEmpty());

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

BOOST_REQUIRE(seqblk_v.size() == 1);

seqlen = kRange.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

s_TestSingleSubjectNuclMask(*seqblk_v.begin());

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, kRange,

));

BOOST_REQUIRE(seqloc_v.begin()->mask.NotEmpty());

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

BOOST_REQUIRE(seqblk_v.size() == 1);

seqlen = kRange.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

s_TestSingleSubjectNuclMask(*seqblk_v.begin());

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, kRange,

));

BOOST_REQUIRE(seqloc_v.begin()->mask.NotEmpty());

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

BOOST_REQUIRE(seqblk_v.size() == 1);

seqlen = kRange.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

s_TestSingleSubjectNuclMask(*seqblk_v.begin());

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, range,

));

unique_ptr<CBlastOptionsHandle>

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

(seqloc_v, opts_handle->GetOptions().GetProgramType(),

seqlen = range.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

BOOST_REQUIRE((*itr)->lcase_mask ==

);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, range,

));

unique_ptr<CBlastOptionsHandle>

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

(seqloc_v, opts_handle->GetOptions().GetProgramType(),

seqlen = range.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

BOOST_REQUIRE((*itr)->lcase_mask ==

);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

unique_ptr<SSeqLoc> sl(m_Om->CreateSSeqLoc(

, range,

));

unique_ptr<CBlastOptionsHandle>

vector<BLAST_SequenceBlk*> seqblk_v;

maxlen = 0;

(seqloc_v, opts_handle->GetOptions().GetProgramType(),

seqlen = range.

();

BOOST_REQUIRE_EQUAL(maxlen, seqlen);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

BOOST_REQUIRE((*itr)->lcase_mask ==

);

(vector<BLAST_SequenceBlk*>, itr, seqblk_v) {

kFile(

);

kSeqIdString(

);

ifstream

(kFile.c_str());

runtime_error(

+ kFile);

read_failed =

;

seq_entry = reader.

();

( read_failed || !seq_entry ) {

runtime_error(

+ kFile);

BOOST_REQUIRE(warnings.empty());

kReplacedPositions[] = { 10+1, 15+1 };

BOOST_REQUIRE_EQUAL((

)kUresidue,

(

)seq.

.

()[kReplacedPositions[

]]);

pair<TSeqPos, TSeqPos> range(0, 19);

unique_ptr<SSeqLoc> sl(

BOOST_REQUIRE_EQUAL(expected_length, seq.

);

pair<TSeqPos, TSeqPos> range(0, 19);

unique_ptr<SSeqLoc> sl(

BOOST_REQUIRE_EQUAL(expected_length, seq.

);

pair<TSeqPos, TSeqPos> range(63999900,64000000);

unique_ptr<SSeqLoc> sl(

hash_value += *sequence;

BOOST_REQUIRE_EQUAL(3285, hash_value);

pair<TSeqPos, TSeqPos> range(3471240, 3686557);

unique_ptr<SSeqLoc> sl(

hash_value += *sequence;

BOOST_REQUIRE_EQUAL(6940529, hash_value);

kNumPrograms = 7;

kProgram[kNumPrograms] =

kNuclDbLength = (

) 39855e+5;

kProtDbLength = (

) 75867e+4;

kNuclNumDbSeqs = (

) 1140e+3;

kProtNumDbSeqs = (

) 2247e+3;

kSearchSp[kNumPrograms] =

{ 2333197e+6, 532990e+5, 423501e+5, 122988e+6, 192228e+6,

532990e+5, 423501e+5 };

kLengthAdjustments[kNumPrograms] =

{ 33, 122, 121, 128, 56, 122, 121 };

kMaxRelativeError = 5e-6;

(index = 0; index < kNumPrograms; ++index) {

query_v.push_back(

(loc, scope));

, strand_opt, msgs);

BOOST_REQUIRE(m->empty());

&sbp, 1.0, &blast_message,

BOOST_REQUIRE(blast_message ==

);

BOOST_REQUIRE(status == 0);

0, 0, &eff_len_params);

db_is_nucl = (kProgram[index] ==

||

(db_is_nucl ? kNuclDbLength : kProtDbLength);

(db_is_nucl ? kNuclNumDbSeqs : kProtNumDbSeqs);

eff_len_params, sbp, query_info,

);

relative_error =

((kSearchSp[index] -

BOOST_REQUIRE(relative_error < kMaxRelativeError);

BOOST_REQUIRE_EQUAL(kLengthAdjustments[index],

relative_error =

((kSearchSp[index] -

BOOST_REQUIRE(relative_error < kMaxRelativeError);

query_v.push_back(*sseqloc);

unique_ptr<CBlastOptionsHandle>

opts_handle->SetOptions().SetGappedMode(

);

s_ValidateProtein130912(qf, opts_handle->GetOptions(),

);

BOOST_REQUIRE(eff_searchsp > 0);

s_ValidateProtein130912(qf, opts_handle->GetOptions(),

);

query_v.push_back(*sseqloc);

unique_ptr<CBlastOptionsHandle>

s_ValidateProtein130912(qf, opts_handle->GetOptions(),

);

BOOST_REQUIRE(eff_searchsp > 0);

s_ValidateProtein130912(qf, opts_handle->GetOptions(),

);

kSearchSp = (

) 1e+9;

kQueryLength = 1000;

(

*)&kSearchSp, 1);

BOOST_REQUIRE_EQUAL(kSearchSp,

query_v.push_back(*sl);

BOOST_REQUIRE_EQUAL((

)1, query_v[0].genetic_code_id);

BOOST_REQUIRE_EQUAL((

)2, query_v[0].genetic_code_id);

query_v.push_back(*sl);

=

(kProgram, qsup_opts, score_opts, query_blk, query_info,

BOOST_REQUIRE_EQUAL(0, (

)

);

BOOST_REQUIRE_EQUAL(-3, sbp->

->

[1][11]);

BOOST_REQUIRE_EQUAL(-2, sbp->

->

[0][11]);

BOOST_REQUIRE(lookup_segments ==

);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE_EQUAL(0, (

)

);

BOOST_REQUIRE_EQUAL(-1, sbp->

->

[1][14]);

BOOST_REQUIRE_EQUAL(-1, sbp->

->

[1][11]);

BOOST_REQUIRE_EQUAL(0, sbp->

->

[0][11]);

BOOST_REQUIRE(lookup_segments ==

);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE_EQUAL(1, (

)

);

BOOST_REQUIRE(lookup_segments ==

);

BOOST_REQUIRE(sbp ==

);

score_opts->

= 3124;

BOOST_REQUIRE_EQUAL(-1, (

)

);

BOOST_REQUIRE(lookup_segments ==

);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(blast_msg ==

);

BOOST_REQUIRE(qsup_opts ==

);

BOOST_REQUIRE(score_opts ==

);

ifstream

(

);

query_v.push_back(

(sl, scope));

s_GetScoringOpts(kOpts),

&sbp, 1.0, &blast_message,

BOOST_REQUIRE(blast_message ==

);

BOOST_REQUIRE(status == 0);

BOOST_REQUIRE(sbp ==

);

BOOST_REQUIRE(status == 0);

CSeq_loc* mask_seqloc =

CSeq_loc(id3, 10, 20,

);

ssl3->mask.Reset(mask_seqloc);

query_v.push_back(*ssl1);

query_v.push_back(*ssl2);

query_v.push_back(*ssl3);

kProgram,

, blast_msg);

BOOST_REQUIRE(lcase_mask !=

);

+= (*qm)->GetMessage();

BOOST_REQUIRE(

.find(

) != string::npos);

nucl_length = nucl_seq.

;

&frame_offsets, &mixed_seq);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[0]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[1]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[2]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[nucl_length+1]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[nucl_length+2]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[nucl_length+3]);

BOOST_REQUIRE_EQUAL(0, (

) mixed_seq[2*nucl_length+2]);

(

index = 0; index <=

; ++index) {

BOOST_REQUIRE_EQUAL(0,

(

) translation_buffer[frame_offsets[index]]);

BOOST_REQUIRE_EQUAL(0, (

)frame_offsets[0]);

BOOST_REQUIRE_EQUAL(nucl_length+1, (

)frame_offsets[3]);

BOOST_REQUIRE_EQUAL(2*nucl_length+2, (

)frame_offsets[

]);

(translation_buffer);

(frame_offsets);

query_v.push_back(*sl);

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

query_v.push_back(*sl);

, strand_opt, blast_msg);

BOOST_REQUIRE(m->empty());

#define COMPRESSION_RATIO

Compression ratio of nucleotide bases (4 bases in 1 byte)

#define sfree(x)

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

#define CODON_LENGTH

Codons are always of length 3.

#define NUM_STRANDS

Number of frames in a nucleotide sequence.

#define NUM_FRAMES

Number of frames to which we translate in translating searches.

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

Declares the BLAST exception class.

BlastMaskLoc * BlastMaskLocFree(BlastMaskLoc *mask_loc)

Deallocate memory for a BlastMaskLoc structure as well as the BlastSeqLoc's pointed to.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)

Deallocates message memory.

Definitions which are dependant on the NCBI C++ Object Manager.

Int2 BlastQuerySetUpOptionsNew(QuerySetUpOptions **options)

Allocate memory for QuerySetUpOptions and fill with default values.

Int2 BlastEffectiveLengthsOptionsNew(BlastEffectiveLengthsOptions **options)

Allocate memory for BlastEffectiveLengthsOptions* and fill with default values.

Int2 BLAST_FillEffectiveLengthsOptions(BlastEffectiveLengthsOptions *options, Int4 dbseq_num, Int8 db_length, Int8 *searchsp_eff, Int4 num_searchsp)

Fill the non-default values in the BlastEffectiveLengthsOptions structure.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

BlastEffectiveLengthsOptions * BlastEffectiveLengthsOptionsFree(BlastEffectiveLengthsOptions *options)

Deallocate memory for BlastEffectiveLengthsOptions*.

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

QuerySetUpOptions * BlastQuerySetUpOptionsFree(QuerySetUpOptions *options)

Deallocate memory for QuerySetUpOptions.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

BlastEffectiveLengthsParameters * BlastEffectiveLengthsParametersFree(BlastEffectiveLengthsParameters *parameters)

Deallocate memory for BlastEffectiveLengthsParameters*.

Int2 BlastEffectiveLengthsParametersNew(const BlastEffectiveLengthsOptions *options, Int8 db_length, Int4 num_seqs, BlastEffectiveLengthsParameters **parameters)

Allocate memory for BlastEffectiveLengthsParameters.

Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p)

Returns true if program is PHI-BLAST (i.e.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_SubjectIsProtein(EBlastProgramType p)

Returns true if the subject is protein.

Boolean Blast_SubjectIsNucleotide(EBlastProgramType p)

Returns true if the subject is nucleotide.

Boolean Blast_QueryIsNucleotide(EBlastProgramType p)

Returns true if the query is nucleotide.

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

Returns true if program is RPS-BLAST (i.e.

EBlastProgramType

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

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

BlastQueryInfo * BlastQueryInfoFree(BlastQueryInfo *query_info)

Deallocate memory for query information structure.

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_MainSetUp(EBlastProgramType program_number, const QuerySetUpOptions *qsup_options, const BlastScoringOptions *scoring_options, BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, double scale_factor, BlastSeqLoc **lookup_segments, BlastMaskLoc **mask, BlastScoreBlk **sbpp, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

"Main" setup routine for BLAST.

Int2 Blast_ScoreBlkMatrixInit(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)

Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified.

Int2 BLAST_CalcEffLengths(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, const BlastEffectiveLengthsParameters *eff_len_params, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Blast_Message **blast_message)

Function to calculate effective query length and db length as well as effective search space.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Blast_KarlinBlk * Blast_KarlinBlkNew(void)

Callocs a Blast_KarlinBlk.

Int2 Blast_KarlinBlkUngappedCalc(Blast_KarlinBlk *kbp, Blast_ScoreFreq *sfp)

Computes the parameters lambda, H K for use in calculating the statistical significance of high-scori...

Int2 Blast_ScoreBlkKbpIdealCalc(BlastScoreBlk *sbp)

Calculates the Karlin-Altschul parameters assuming standard residue compositions for the query and su...

Int2 Blast_KarlinBlkCopy(Blast_KarlinBlk *kbp_to, Blast_KarlinBlk *kbp_from)

Copies contents of one Karlin block to another.

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

Definitions of special type used in BLAST.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ eBlastp

Protein-Protein.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ ePSITblastn

PSI Tblastn.

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

BLAST_SequenceBlk * BlastSequenceBlkFree(BLAST_SequenceBlk *seq_blk)

Deallocate memory for a sequence block.

Int2 BLAST_CreateMixedFrameDNATranslation(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info)

Initialize the mixed-frame sequence for out-of-frame gapped extension.

Int1 BLAST_ContextToFrame(EBlastProgramType prog_number, Uint4 context_number)

This function translates the context number of a context into the frame of the sequence.

Int2 BLAST_GetAllTranslations(const Uint1 *nucl_seq, EBlastEncoding encoding, Int4 nucl_length, const Uint1 *genetic_code, Uint1 **translation_buffer_ptr, Uint4 **frame_offsets_ptr, Uint1 **mixed_seq_ptr)

Translate nucleotide into 6 frames.

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

BOOST_AUTO_TEST_CASE(NumberOfContextsBlastp)

ncbi::TMaskedQueryRegions mask

CAutoEnvironmentVariable –.

Wrapper class for BLAST_SequenceBlk .

const CSeq_id * GetFirstId() const

Defines BLAST error codes (user errors included)

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

Wrapper class for BlastQueryInfo .

~CBlastSetupTestFixture()

static BlastScoringOptions * s_GetScoringOpts(const CBlastOptions &opts)

static void s_ValidateProtein130912(CRef< IQueryFactory > query_factory, const CBlastOptions &opts, string prefix)

Auxiliary function to validate that the query sequence data hasn't been modified (filtering can chang...

static void s_TestSingleSubjectNuclMask(BLAST_SequenceBlk const *seqblk)

static BlastEffectiveLengthsOptions * s_GetEffLenOpts(const CBlastOptions &opts)

Auxiliary class to compute the effective search space.

Base class for reading FASTA sequences.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

This class wraps the C++ Object Manager to control its lifetime and to facilitate the creation of SSe...

static CTestObjMgr & Instance()

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.

Declares auxiliary class to calculate the effective search space.

Operators to edit gaps in sequences.

#define test(a, b, c, d, e)

static const char *const strings[]

Defines the interface to interact with the genetic code singleton object.

void GenCodeSingletonFini()

Uninitialize the genetic code singleton.

void GenCodeSingletonInit()

Initialize the genetic code singleton.

TSeqPos length

Length of the buffer above (not necessarily sequence length!)

void SetupSubjects(TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Sets up internal subject data structure for the BLAST search.

EBlastEncoding

Different types of sequence encodings for sequence retrieval from the BLAST database.

TAutoUint1ArrayPtr FindGeneticCode(int genetic_code)

Retrieves the requested genetic code in Ncbistdaa format.

void SetGapOpeningCost(int g)

void SetupQueries(TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.

objects::ENa_strand GetStrandOption() const

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

void SetGapExtensionCost(int e)

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

void SetMatrixName(const char *matrix)

BlastEffectiveLengthsOptions * GetEffLenOpts() const

Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

TAutoUint1Ptr data

Sequence data.

BLAST_SequenceBlk * Get() const

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

BlastScoringOptions * GetScoringOpts() const

Returns BlastScoringOptions for eLocal objects, NULL for eRemote.

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

Returns the path to a specified matrix.

unsigned int GetNumberOfContexts(EBlastProgramType p)

Returns the number of contexts for a given BLAST program.

void SetupQueryInfo(TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

Allocates the query information structure and fills the context offsets, in case of multiple queries,...

void Blast_FindDustFilterLoc(TSeqLocVector &queries, const CBlastNucleotideOptionsHandle *nucl_handle)

Finds dust locations for a given set of sequences by calling the the symmetric dust lib.

string Blast_ProgramNameFromType(EBlastProgramType program)

Returns a string program name, given a blast::EBlastProgramType enumeration.

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

Int8 GetEffSearchSpace(size_t query_index=0) const

Retrieve the effective search space calculated for a given query.

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

@ eBlastEncodingNcbi4na

NCBI4na.

@ eBlastEncodingProtein

NCBIstdaa.

@ eBlastEncodingNcbi2na

NCBI2na.

@ eNoSentinels

Do not use sentinel bytes.

@ eSentinels

Use sentinel bytes.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define MSerial_AsnText

I/O stream manipulators –.

CRef< CSeq_entry > ReadSet(int max_seqs=kMax_Int, ILineErrorListener *pMessageListener=nullptr)

Read multiple sequences (by default, as many as are available.)

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

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

int64_t Int8

8-byte (64-bit) signed integer

int8_t Int1

1-byte (8-bit) signed integer

position_type GetLength(void) const

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

@ e_Gi

GenInfo Integrated Database.

const TSeq & GetSeq(void) const

Get the variant data.

unsigned int

A callback function used to compare two keys in a database.

vector< EBlastProgramType > GetAllBlastProgramTypes()

Magic spell ;-) needed for some weird compilers... very empiric.

#define DIM(A)

dimension of an array.

#define FALSE

bool replacment for C indicating false.

std::istream & in(std::istream &in_, double &x_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

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

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

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to hold a sequence.

Uint4 num_seq_ranges

Number of elements in seq_ranges.

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.

Uint1 * sequence

Sequence used for search (could be translation).

Uint1 * oof_sequence

Mixed-frame protein representation of a nucleotide sequence for out-of-frame alignment.

Int4 query_length

Length of this query, strand or frame.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

Int4 length_adjustment

Length adjustment for boundary conditions.

Int8 eff_searchsp

Effective search space for this context.

Options for setting up effective lengths and search spaces.

Parameters for setting up effective lengths and search spaces.

Int8 real_db_length

Total database length to use in search space calculations.

Int4 real_num_seqs

Number of subject sequences to use for search space calculations.

Structure for keeping the query masking information.

BlastSeqLoc ** seqloc_array

Array of masked locations.

The query related information.

BlastContextInfo * contexts

Information per context.

Structure used for scoring calculations.

Blast_ScoreFreq ** sfp

score frequencies for scoring matrix.

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

SBlastScoreMatrix * matrix

scoring matrix data

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

Blast_KarlinBlk ** kbp_gap_std

K-A parameters for std (not position-based) alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Int2 penalty

Penalty for a mismatch.

Int4 gap_open

Extra penalty for starting a gap.

Int4 gap_extend

Penalty for each gap residue.

Int2 reward

Reward for a match.

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

SSeqRange * ssr

location data on the sequence.

Structure to hold the Karlin-Altschul parameters.

Structure to hold the a message from the core of the BLAST engine.

Options required for setting up the query sequence.

int ** data

actual scoring matrix data, stored in row-major form

Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array ...

Structure to represent a single sequence to be fed to BLAST.

Int4 left

left endpoint of range (zero based)

Int4 right

right endpoint of range (zero based)

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

void g_IgnoreDataFile(const string &pattern, bool do_ignore=true)

Ignore (or stop ignoring, depending on do_ignore) NCBI application data files matching the given patt...

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