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

;

kQuerySize = 10;

kNumSeqs = 2;

[] = { 3, 9, 14, 20, 6, 23, 1, 7, 16, 5 };

m_query =

[kQuerySize];

memcpy((

*) m_query, (

*)

, kQuerySize*

(*

));

m_dim.query_length = kQuerySize;

m_dim.num_seqs = kNumSeqs;

(

= 0;

< m_dim.query_length;

++) {

(

j = 0; j < m_dim.num_seqs+1; j++) {

m_msa->data[j][

].letter =

[

];

m_msa->data[j][

].is_aligned =

;

m_msa->data[1][0].letter =

m_msa->data[2][0].letter =

m_msa->data[2][m_dim.query_length-1].letter =

memset((

*) &m_diag_request, 0,

(m_diag_request));

&m_diag_request;

(

= 0;

< m_dim.query_length;

++) {

(

j = 0; j < m_dim.num_seqs+1; j++) {

m_msa->data[j][

].letter = m_query[

];

m_msa->data[j][

].is_aligned =

;

gap_position =

.GetRand(0, GetQueryLength() - 1);

m_msa->data[0][gap_position].letter = m_query[gap_position];

memcpy((

*)&m_options, (

*)opts,

(

));

eNearIdenticalHits:

SetupNearIdenticalHits();

eMsaHasUnalignedRegion:

SetupMsaHasUnalignedRegion();

eQueryAlignedWithInternalGaps:

SetupQueryAlignedWithInternalGaps();

eHenikoffsPaper:

SetupHenikoffsPositionBasedSequenceWeights();

std::logic_error(

);

kQueryLength = 232;

kNumAlignedSeqs = 1;

m_dim.query_length = kQueryLength;

m_dim.num_seqs = kNumAlignedSeqs;

m_query =

[kQueryLength];

(

= 0;

< kQueryLength;

++) {

(

seq_idx = 0; seq_idx < kNumAlignedSeqs + 1;

m_msa->data[seq_idx][

].letter = m_query[

] =

[

];

m_msa->data[seq_idx][

].is_aligned =

;

BOOST_REQUIRE(score_matrix);

(score > max_score) {

kNumAlignedSeqs = 2;

m_dim.query_length = kQueryLength;

m_dim.num_seqs = kNumAlignedSeqs;

m_query =

[kQueryLength];

(

= 0;

< kQueryLength;

++) {

m_msa->data[0][

].letter = m_query[

] =

[

];

m_msa->data[0][

].is_aligned =

;

(

= kFirstAlignment.first;

< kFirstAlignment.second;

++) {

m_msa->data[1][

].letter =

FindNonIdenticalHighScoringResidue(

[

], score_matrix);

m_msa->data[1][

].is_aligned =

;

(

= kSecondAlignment.first;

< kSecondAlignment.second;

++) {

m_msa->data[2][

].letter =

FindNonIdenticalHighScoringResidue(

[

], score_matrix);

m_msa->data[2][

].is_aligned =

;

kNumAlignedSeqs = 1;

kLocalQueryLength = 87;

m_dim.query_length = kLocalQueryLength;

m_dim.num_seqs = kNumAlignedSeqs;

m_query =

[kLocalQueryLength];

query_seq(

);

query_seq +=

(

);

query_seq +=

(

);

pair<TAlignedSegment, string> TAlignedSequence;

vector<TAlignedSequence> aligned_sequence;

TAlignedSequence region(make_pair(make_pair(0

, 8U),

(

)));

aligned_sequence.push_back(region);

region = make_pair(make_pair(12U, 39U),

(

));

aligned_sequence.push_back(region);

region = make_pair(make_pair(41U, 57U),

(

));

aligned_sequence.push_back(region);

region = make_pair(make_pair(62U, 71U),

(

));

aligned_sequence.push_back(region);

region = make_pair(make_pair(72U, 87U),

(

));

aligned_sequence.push_back(region);

(

= 0;

< kLocalQueryLength;

++) {

query_seq.substr(

, 1));

m_msa->data[0][

].letter = m_query[

];

m_msa->data[0][

].is_aligned =

;

m_msa->data[1][

].letter = kGapResidue;

m_msa->data[1][

].is_aligned =

;

(vector<TAlignedSequence>, itr, aligned_sequence) {

sequence_data = itr->second;

(

= loc.first, j = 0;

< loc.second;

++, j++) {

m_msa->data[1][

].letter =

sequence_data.substr(j, 1));

kNumAlignedSeqs = 3;

kQuerySequence[5] = { 7, 22, 19, 7, 17 };

kSeq1[5] = { 7, 6, 4, 7, 6 };

kSeq2[5] = { 7, 22, 4, 7, 6 };

kSeq3[5] = { 7, 22, 15, 7, 7 };

m_dim.query_length =

(

);

m_dim.num_seqs = kNumAlignedSeqs;

m_query =

[

(kQuerySequence)];

(

s = 0; s < kNumAlignedSeqs; s++) {

0: sequence = kSeq1;

;

1: sequence = kSeq2;

;

2: sequence = kSeq3;

;

(

= 0;

<

(kQuerySequence);

++) {

m_query[

] = kQuerySequence[

];

m_msa->data[s][

].letter = sequence[

];

m_msa->data[s][

].is_aligned =

;

kNumAlignedSeqs = 2;

kGi_129296_[388] = {

12, 4, 17, 9, 17, 19, 18, 13, 1, 10, 6, 3, 6, 4, 19,

6, 13, 5, 12, 10, 19, 8, 8, 19, 13, 5, 13, 9, 11, 22,

3, 14, 11, 17, 9, 11, 18, 1, 11, 1, 12, 19, 22, 11, 7,

1, 16, 7, 13, 18, 5, 17, 15, 12, 10, 10, 19, 11, 8, 6,

4, 17, 9, 18, 7, 1, 7, 17, 18, 18, 4, 17, 15, 3, 7,

17, 17, 5, 22, 19, 8, 13, 11, 6, 10, 5, 11, 11, 17, 5,

9, 18, 16, 14, 13, 1, 18, 22, 17, 11, 5, 9, 1, 4, 10,

11, 22, 19, 4, 10, 18, 6, 17, 19, 11, 14, 5, 22, 11, 17,

3, 1, 16, 10, 6, 22, 18, 7, 7, 19, 5, 5, 19, 13, 6,

10, 18, 1, 1, 5, 5, 1, 16, 15, 11, 9, 13, 17, 20, 19,

5, 10, 5, 18, 13, 7, 15, 9, 10, 4, 11, 11, 19, 17, 17,

17, 9, 4, 6, 7, 18, 18, 12, 19, 6, 9, 13, 18, 9, 22,

6, 10, 7, 9, 20, 10, 9, 1, 6, 13, 18, 5, 4, 18, 16,

5, 12, 14, 6, 17, 12, 18, 10, 5, 5, 17, 10, 14, 19, 15,

12, 12, 3, 12, 13, 13, 17, 6, 13, 19, 1, 18, 11, 14, 1,

5, 10, 12, 10, 9, 11, 5, 11, 14, 22, 1, 17, 7, 4, 11,

17, 12, 11, 19, 11, 11, 14, 4, 5, 19, 17, 7, 11, 5, 16,

9, 5, 10, 18, 9, 13, 6, 4, 10, 11, 16, 5, 20, 18, 17,

18, 13, 1, 12, 1, 10, 10, 17, 12, 10, 19, 22, 11, 14, 16,

12, 10, 9, 5, 5, 10, 22, 13, 11, 18, 17, 9, 11, 12, 1,

11, 7, 12, 18, 4, 11, 6, 17, 16, 17, 1, 13, 11, 18, 7,

9, 17, 17, 19, 4, 13, 11, 12, 9, 17, 4, 1, 19, 8, 7,

19, 6, 12, 5, 19, 13, 5, 5, 7, 18, 5, 1, 18, 7, 17,

18, 7, 1, 9, 7, 13, 9, 10, 8, 17, 11, 5, 11, 5, 5,

6, 16, 1, 4, 8, 14, 6, 11, 6, 6, 9, 16, 22, 13, 14,

18, 13, 1, 9, 11, 6, 6, 7, 16, 22, 20, 17, 14};

m_dim.query_length = kQueryLength;

m_dim.num_seqs = kNumAlignedSeqs;

m_query =

[kQueryLength];

(

= 0;

< kQueryLength;

++) {

(

= 1;

< kNumAlignedSeqs + 1;

++) {

(

j = 0; j < kQueryLength; j++) {

m_msa->data[

][j].letter = kGi_129296_[j];

m_msa->data[

][j].is_aligned =

;

kHitIndex = 2;

kNumIdenticalResidues = (

) (GetQueryLength() *

(

= kNumIdenticalResidues;

< GetQueryLength();

++) {

& residue = m_msa->data[kHitIndex][

].letter;

15, 9, 10, 4, 11, 11, 19, 17, 17, 17, 18, 4, 11, 4, 18,

18, 11, 19, 11, 19, 13, 1, 9, 22, 6, 10, 7, 12, 20, 10,

18, 1, 6, 13, 1, 5, 4, 18, 16, 5, 12, 14, 6, 8, 19,

18, 10, 15, 5, 17, 10, 14, 19, 15, 12, 12, 3, 12, 13, 13,

17, 6, 13, 19, 1, 18, 11, 14, 1, 5, 10, 12, 10, 9, 11,

5, 11, 14, 6, 1, 17, 7, 4, 11, 17, 12, 11, 19, 11, 11,

14, 4, 5, 19, 17, 4, 11, 5, 16, 9, 5, 10, 18, 9, 13,

6, 5, 10, 11, 18, 5, 20, 18, 13, 14, 13, 18, 12, 5, 10,

16, 16, 19, 10, 19, 22, 11, 14, 15, 12, 10, 9, 5, 5, 10,

22, 13, 11, 18, 17, 19, 11, 12, 1, 11, 7, 12, 18, 4, 11,

6, 9, 14, 17, 1, 13, 11, 18, 7, 9, 17, 17, 1, 5, 17,

11, 10, 9, 17, 15, 1, 19, 8, 7, 1, 6, 12, 5, 11, 17,

5, 4, 7, 9, 5, 12, 1, 7, 17, 18, 7, 19, 9, 5, 4,

9, 10, 8, 17, 14, 5, 17, 5, 15, 6, 16, 1, 4, 8, 14,

6, 11, 6, 11, 9, 10, 8, 13, 14, 18, 13, 18, 9, 19, 22,

6, 7, 16, 22, 20, 17, 14};

seqalign(

);

unique_ptr<CObjectIStream>

qid(

), sid(

);

memset((

*) &request, 0,

(request));

request.

=

;

(

);

((*iter)->IsTitle()) {

query_descr += (*iter)->GetTitle();

BOOST_REQUIRE_EQUAL(query_descr,

);

kNumElements =

BOOST_REQUIRE_EQUAL(kNumElements, res_freqs.size());

BOOST_REQUIRE_EQUAL(kNumElements, wres_freqs.size());

BOOST_REQUIRE_EQUAL(kNumElements, freq_ratios.size());

qid(

), sid(

);

BOOST_REQUIRE(sasv.size() != 0);

unique_ptr<CPsiBlastInputData> pssm_input(

sasv[0], q->scope, *opts));

pssm_input->Process();

vector<PSIMsaCell> aligned_pos(pssm_input->GetQueryLength());

fill(aligned_pos.begin(), aligned_pos.end(), kNullPSIMsaCell);

& ds = (*hsp)->GetSegs().GetDenseg();

vector<TSignedSeqPos>& starts = ds.

();

vector<TSeqPos>& lengths = ds.

();

(

pos = 0; pos < lengths[

]; pos++) {

s_index += lengths[

];

s_index = (

== 0) ? 0 : (s_index - starts[1]);

(

pos = 0; pos < lengths[

]; pos++) {

pd.

= subj[s_index++];

(

= 0;

< pssm_input->GetQueryLength();

++) {

BOOST_REQUIRE(seq_index < nseqs);

pssm_input->GetData()->data[seq_index][

];

ss <<

<< seq_index <<

<<

BOOST_REQUIRE_MESSAGE(aligned_pos[

].

== pos_desc.

&&

aligned_pos[

].is_aligned == pos_desc.

, ss.str());

}

(

exception& e) {

cerr << e.what() << endl;

BOOST_REQUIRE(

);

cerr <<

<< endl;

BOOST_REQUIRE(

);

unique_ptr<IPssmInputData> pssm_input

pssm_input->Process();

kSelfHitIndex = 1;

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[

]);

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[kSelfHitIndex]);

unique_ptr<IPssmInputData> pssm_input

pssm_input->Process();

kDuplicateHitIndex = 2;

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[kDuplicateHitIndex]);

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[

]);

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[

+ 1]);

unique_ptr<IPssmInputData> pssm_input

pssm_input->Process();

kRemovedHitIndex = 2;

BOOST_REQUIRE_EQUAL(

,

!! msa->use_sequence[kRemovedHitIndex]);

BOOST_REQUIRE_EQUAL(

, !!msa->use_sequence[

]);

BOOST_REQUIRE_EQUAL(

, !! msa->use_sequence[

+ 1]);

unique_ptr<IPssmInputData> pssm_input

BOOST_REQUIRE_EQUAL(

(

),

(pssm_input->GetMatrixName()));

unique_ptr< CNcbiMatrix<int> > pssm

(

)pssm->GetCols());

(

)pssm->GetRows());

(

= 0;

< pssm_asn->

().GetNumColumns();

++) {

(

j = 0; j < pssm_asn->

().GetNumRows(); j++) {

(pssm_input->GetData()->data[1][

].is_aligned

&& pssm_input->GetData()->data[1][

].letter != kGapResidue) {

(j == kGapResidue || j == kBResidue || j == kZResidue

|| j == kUResidue || j >= kOResidue) {

ss <<

<<

<<

pssm_input->GetQuery()[

], j);

ss <<

<<

<<

BOOST_REQUIRE_MESSAGE (score - (*pssm)(j,

) <= 3, ss.str());

unique_ptr<IPssmInputData> pssm_input

pssm_input->Process();

BOOST_REQUIRE_EQUAL(

(

),

(pssm_input->GetMatrixName()));

BOOST_REQUIRE_EQUAL(

,

BOOST_REQUIRE_EQUAL(

, !! packed_msa->use_sequence[1]);

BOOST_REQUIRE_EQUAL(

, !! packed_msa->use_sequence[2]);

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

vector<CPssmInputTestData::TAlignedSegment> aligned_regions;

aligned_regions.push_back(make_pair(0

, 99U));

aligned_regions.push_back(make_pair(200U,

pssm_input->GetQueryLength()-1));

(vector<CPssmInputTestData::TAlignedSegment>::const_iterator

=

aligned_regions.begin();

!= aligned_regions.end(); ++

) {

(

pos =

->first; pos < i->second; pos++) {

ss <<

BOOST_REQUIRE_MESSAGE((

)

->first == (

)aligned_blocks->pos_extnt[pos].left, ss.str());

BOOST_REQUIRE_MESSAGE((

)

->second == (

)aligned_blocks->pos_extnt[pos].right, ss.str());

BOOST_REQUIRE_MESSAGE( (

)(

->second -

->first + 1) == (

)aligned_blocks->size[pos], ss.str());

(

= kUnalignedRange.first;

< kUnalignedRange.second;

++) {

ss <<

BOOST_REQUIRE_MESSAGE((

)-1 == (

)aligned_blocks->pos_extnt[

].left, ss.str());

BOOST_REQUIRE_MESSAGE( (

)pssm_input->GetQueryLength() == (

)aligned_blocks->pos_extnt[

].right, ss.str());

BOOST_REQUIRE_MESSAGE(

(

)(aligned_blocks->pos_extnt[

].right - aligned_blocks->pos_extnt[

].left + 1) == (

)aligned_blocks->size[

],

pssm_input->GetQueryLength()));;

(query_with_sentinels.get(), pssm_input->GetQueryLength()));

seq_weights.

());

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

(vector<CPssmInputTestData::TAlignedSegment>::const_iterator

=

aligned_regions.begin();

!= aligned_regions.end(); ++

) {

(

pos =

->first; pos < i->second; pos++) {

total_sequence_weights_for_column = 0.0;

(

res = 0; res < msa->alphabet_size; res++) {

(res == kXResidue)

;

total_sequence_weights_for_column +=

seq_weights->match_weights[pos][res];

BOOST_REQUIRE(total_sequence_weights_for_column > 0.99 &&

total_sequence_weights_for_column < 1.01);

(

pos = kUnalignedRange.first;

pos < kUnalignedRange.second; pos++) {

total_sequence_weights_for_column = 0.0;

(

res = 0; res < msa->alphabet_size; res++) {

(res == kXResidue)

;

total_sequence_weights_for_column +=

seq_weights->match_weights[pos][res];

BOOST_REQUIRE(total_sequence_weights_for_column == 0.0);

internal_pssm.

());

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

seq_weights->std_prob);

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

seq_weights->std_prob,

internal_pssm.

(),

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

BOOST_REQUIRE_EQUAL(msa->dimensions->num_seqs, 3u);

(

= 0;

< pssm_input->GetQueryLength();

++) {

(msa->cell[1][

].is_aligned || msa->cell[2][

].is_aligned

|| msa->cell[3][

].is_aligned) {

(j == kBResidue || j == kZResidue || j == kUResidue

|| j >= kOResidue) {

(j == kGapResidue) {

ss <<

<<

<<

BOOST_REQUIRE_MESSAGE(

== internal_pssm->pssm[

][j], ss.str());

ss <<

<<

<<

BOOST_REQUIRE_MESSAGE(score-1 <= internal_pssm->pssm[

][j] && internal_pssm->pssm[

][j] <= score+1, ss.str());

unique_ptr<IPssmInputData> pssm_input

pssm_input->Process();

BOOST_REQUIRE_EQUAL(

(

),

(pssm_input->GetMatrixName()));

kSelfHitIndex = 1;

BOOST_REQUIRE_EQUAL(

,

BOOST_REQUIRE_EQUAL(

,

!! packed_msa->use_sequence[kSelfHitIndex]);

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

(

= 0;

< pssm_input->GetQueryLength();

++) {

BOOST_REQUIRE_EQUAL((

)-1,

(

)aligned_blocks->pos_extnt[

].left);

BOOST_REQUIRE_EQUAL((

)pssm_input->GetQueryLength(),

(

)aligned_blocks->pos_extnt[

].right);

BOOST_REQUIRE_EQUAL((

)pssm_input->GetQueryLength() + 2,

(

)aligned_blocks->size[

]);

pssm_input->GetQueryLength()));;

(query_with_sentinels.get(), pssm_input->GetQueryLength()));

seq_weights.

());

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

internal_pssm.

());

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

seq_weights->std_prob);

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

seq_weights->std_prob,

internal_pssm.

(),

ss <<

BOOST_REQUIRE_MESSAGE(

== rv, ss.str());

(

= 0;

< pssm_input->GetQueryLength();

++) {

(j == kGapResidue || j == kBResidue || j == kZResidue

|| j == kUResidue || j >= kOResidue) {

ss <<

<<

<<

BOOST_REQUIRE_MESSAGE(

== internal_pssm->pssm[

][j], ss.str());

ss <<

<<

<<

BOOST_REQUIRE_MESSAGE(score-1 <= internal_pssm->pssm[

][j] && internal_pssm->pssm[

][j] <= score+1, ss.str());

unique_ptr<IPssmInputData> bad_pssm_data(

());

unique_ptr<IPssmInputData> bad_pssm_data(

BOOST_REQUIRE(msa ==

);

BOOST_REQUIRE(freq_ratios !=

);

BOOST_REQUIRE(freq_ratios ==

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the CBl2Seq (BLAST 2 Sequences) class.

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

Declares the BLAST exception class.

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

PSIBlastOptions * PSIBlastOptionsFree(PSIBlastOptions *psi_options)

Deallocate PSI BLAST options.

#define BLAST_EXPECT_VALUE

Default parameters for saving hits.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

Port of posit.h structures and impalaScaling for implementing composition based statistics for PSI-BL...

PSIMsa * PSIMsaFree(PSIMsa *msa)

Deallocates the PSIMsa structure.

PSIMsa * PSIMsaNew(const PSIMsaDimensions *dimensions)

Allocates and initializes the multiple sequence alignment data structure for use as input to the PSSM...

int _PSIComputeAlignmentBlocks(const _PSIMsa *msa, _PSIAlignedBlock *aligned_blocks)

Main function to compute aligned blocks' properties for each position within multiple alignment (stag...

int _PSIConvertFreqRatiosToPSSM(_PSIInternalPssmData *internal_pssm, const Uint1 *query, const BlastScoreBlk *sbp, const double *std_probs)

Converts the PSSM's frequency ratios obtained in the previous stage to a PSSM of scores.

int _PSIComputeFreqRatios(const _PSIMsa *msa, const _PSISequenceWeights *seq_weights, const BlastScoreBlk *sbp, const _PSIAlignedBlock *aligned_blocks, Int4 pseudo_count, Boolean nsg_compatibility_mode, _PSIInternalPssmData *internal_pssm)

Main function to compute the PSSM's frequency ratios (stage 5).

_PSISequenceWeights * _PSISequenceWeightsNew(const PSIMsaDimensions *dimensions, const BlastScoreBlk *sbp)

Allocates and initializes the _PSISequenceWeights structure.

_PSIInternalPssmData * _PSIInternalPssmDataNew(Uint4 query_length, Uint4 alphabet_size)

Allocates a new _PSIInternalPssmData structure.

_PSIAlignedBlock * _PSIAlignedBlockNew(Uint4 query_length)

Allocates and initializes the _PSIAlignedBlock structure.

int _PSIComputeSequenceWeights(const _PSIMsa *msa, const _PSIAlignedBlock *aligned_blocks, Boolean nsg_compatibility_mode, _PSISequenceWeights *seq_weights)

Main function to calculate the sequence weights.

int _PSIPurgeBiasedSegments(_PSIPackedMsa *msa)

Main function for keeping only those selected sequences for PSSM construction (stage 2).

_PSIMsa * _PSIMsaNew(const _PSIPackedMsa *msa, Uint4 alphabet_size)

Allocates and initializes the internal version of the PSIMsa structure (makes a deep copy) for intern...

const double kPSINearIdentical

Percent identity threshold for discarding near-identical matches.

const unsigned int kQueryIndex

Index into multiple sequence alignment structure for the query sequence.

int _PSIScaleMatrix(const Uint1 *query, const double *std_probs, _PSIInternalPssmData *internal_pssm, BlastScoreBlk *sbp)

Scales the PSSM (stage 7)

_PSIPackedMsa * _PSIPackedMsaNew(const PSIMsa *msa)

Allocates and initializes the compact version of the PSIMsa structure (makes a deep copy) for interna...

Private interface for Position Iterated BLAST API, contains the PSSM generation engine.

#define PSIERR_BADPARAM

Bad parameter used in function.

#define PSI_SUCCESS

Successful operation.

Utilities initialize/setup BLAST.

#define BLAST_SCORE_MIN

minimum allowed score (for one letter comparison).

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

@ eBlastp

Protein-Protein.

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

TSeqPos GetLength(void) const

Runs the BLAST algorithm between 2 sequences.

Defines BLAST error codes (user errors included)

Wrapper class for BlastScoreBlk .

Mock object for the PSSM input data which returns NULLs for all its methods.

PSIMsa * GetData()

Obtain the multiple sequence alignment structure.

unsigned int GetQueryLength()

Get the query's length.

unsigned char * GetQuery()

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

const PSIDiagnosticsRequest * GetDiagnosticsRequest()

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in t...

const PSIBlastOptions * GetOptions()

Obtain the options for the PSSM engine.

void Process()

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

const char * GetMatrixName()

Obtain the name of the underlying matrix to use when building the PSSM.

Wrapper class for PSIBlastOptions .

This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST alg...

This class exists merely to call private methods in CPsiBlastInputData and CPssmEngine.

static unsigned int GetNumAlignedSequences(const CPsiBlastInputData &input)

Accesses CPsiBlastInputData private method.

static string x_ErrorCodeToString(int error_code)

Gets error strings from a CPssmEngine private method.

static unsigned char * x_GuardProteinQuery(const unsigned char *query, unsigned int query_length)

Accesses CPssmEngine private method.

static void x_GetSubjectSequence(const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)

Gets Subject sequence from a CPsiBlastInputData private method.

Exception class for the CPssmEngine class.

Computes a PSSM as specified in PSI-BLAST.

Mock object for the PSSM input data which returns multiple sequence alignment data which has flanking...

const PSIBlastOptions * GetOptions()

Obtain the options for the PSSM engine.

void Process()

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

PSIMsa * GetData()

Obtain the multiple sequence alignment structure.

PSIBlastOptions * m_options

PSIDiagnosticsRequest m_diag_request

const PSIDiagnosticsRequest * GetDiagnosticsRequest()

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in t...

virtual ~CPssmInputFlankingGaps()

unsigned int GetQueryLength()

Get the query's length.

unsigned char * GetQuery()

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

Mock object for the PSSM input data which returns a query sequence with a gap in it.

Mock object for the PSSM input data which returns a query sequence with a gap in it.

unsigned int GetQueryLength()

Get the query's length.

Mock object for the PSSM input data which can be configured to have different combinations of aligned...

CPssmInputTestData(EAlignmentType type, PSIBlastOptions *opts=NULL)

pair< TSeqPos, TSeqPos > TAlignedSegment

void SetupDuplicateHit(void)

@ eQueryAlignedWithInternalGaps

void SetupHenikoffsPositionBasedSequenceWeights(void)

Uint1 FindNonIdenticalHighScoringResidue(Uint1 res, const SNCBIPackedScoreMatrix *score_matrix)

void SetupNearIdenticalHits(void)

static const size_t kQueryLength

void SetupQueryAlignedWithInternalGaps()

static const Uint1 kQuery[kQueryLength]

void SetupMsaHasUnalignedRegion(void)

const char * GetMatrixName()

Obtain the name of the underlying matrix to use when building the PSSM.

static TIndex GetIndex(CSeq_data::E_Choice code_type, const string &code)

static CTestObjMgr & Instance()

TSeqPos length

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

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

static CNcbiMatrix< int > * GetScores(const objects::CPssmWithParameters &pssm)

Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastS...

#define BLASTAA_SIZE

Size of aminoacid alphabet.

TAutoUint1Ptr data

Sequence data.

virtual TSeqAlignVector Run()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as fo...

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

void Reset(BlastScoreBlk *p=NULL)

AutoPtr< Uint1, CDeleter< Uint1 > > TAutoUint1Ptr

Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc)

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.

@ eBlastEncodingProtein

NCBIstdaa.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

element_type * get(void) const

Get pointer.

@ eSerial_AsnText

ASN.1 text.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

Uint4 TValue

Type of the generated integer value and/or the seed value.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

const TFreqRatios & GetFreqRatios(void) const

Get the FreqRatios member data.

TNumRows GetNumRows(void) const

Get the NumRows member data.

const TWeightedResFreqsPerPos & GetWeightedResFreqsPerPos(void) const

Get the WeightedResFreqsPerPos member data.

list< int > TResFreqsPerPos

TNumColumns GetNumColumns(void) const

Get the NumColumns member data.

list< double > TWeightedResFreqsPerPos

const TIntermediateData & GetIntermediateData(void) const

Get the IntermediateData member data.

list< double > TFreqRatios

const TResFreqsPerPos & GetResFreqsPerPos(void) const

Get the ResFreqsPerPos member data.

const TPssm & GetPssm(void) const

Get the Pssm member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

list< CRef< CSeqdesc > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ e_Ncbistdaa

consecutive codes for std aas

unsigned int

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

SFreqRatios * _PSIMatrixFrequencyRatiosFree(SFreqRatios *freq_ratios)

Deallocate the frequency ratios structure.

SFreqRatios * _PSIMatrixFrequencyRatiosNew(const char *matrix_name)

Retrive the matrix's frequency ratios.

const TYPE & Get(const CNamedParameterList *param)

char GetResidue(unsigned int res)

Returns character representation of a residue from ncbistdaa.

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

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.

Declarations of auxiliary functions/classes for PSI-BLAST.

C++ API for the PSI-BLAST PSSM engine.

Defines interface for a sequence alignment processor that can populate a multiple alignment data stru...

BlastScoreBlk * InitializeBlastScoreBlk(const unsigned char *query, Uint4 query_size)

Utilities to develop and debug unit tests that deal with PSSM computation.

BOOST_AUTO_TEST_CASE(testFullPssmEngineRunWithDiagnosticsRequest)

const SNCBIPackedScoreMatrix NCBISM_Blosum62

TNCBIScore NCBISM_GetScore(const SNCBIPackedScoreMatrix *sm, int aa1, int aa2)

Look up an entry in a packed score matrix.

Int2 alphabet_size

size of alphabet.

Abstract base class to encapsulate the source(s) and pre-processing of PSSM input data as well as opt...

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Boolean nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure gr...

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

Int4 pseudo_count

Pseudocount constant.

Boolean use_best_alignment

If set to TRUE, use the best alignment when multiple HSPs are found in a query-subject alignment (i....

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

Boolean information_content

request information content

Boolean frequency_ratios

request frequency ratios

Boolean weighted_residue_frequencies

request observed weighted residue frequencies

Boolean gapless_column_weights

request gapless column weights

Boolean num_matching_seqs

request number of matching sequences

Boolean sigma

request sigma

Boolean residue_frequencies

request observed residue frequencies

Boolean interval_sizes

request interval sizes

Structure to describe the characteristics of a position in the multiple sequence alignment data struc...

Boolean is_aligned

Is this letter part of the alignment?

Uint1 letter

Preferred letter at this position, in ncbistdaa encoding.

Structure representing the dimensions of the multiple sequence alignment data structure.

Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to...

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

Stores the frequency ratios along with their bit scale factor.

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

static const string kTitle

CTraceGlyph inline method implementation.

static Uint4 letter(char c)

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