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NCBI C++ ToolKit: src/algo/cobalt/unit_test/cobalt_unit_test.cpp Source File

BOOST_REQUIRE(it->NotEmpty());

BOOST_REQUIRE(!archive.

());

((

)expected_hits.size() != hitlist.

()) {

err +=

+

;

(

=0;

<

(expected_hits.size(), (

)hitlist.

());

->CompareOrdered(expected_query_id) != 0) {

err += header +

+ expected_hits[

].query

->GetId()->AsFastaString() +

;

err += header +

+

;

(expected_hits[

].query_range.GetFrom()

|| expected_hits[

].query_range.GetTo()

err += header +

+

;

(expected_hits[

].subject_range.GetFrom()

|| expected_hits[

].subject_range.GetTo()

err += header +

+

;

(expected_hits[

].score != hit->

) {

err += header +

+

;

kParseDeflines =

;

);

kParseDeflines =

;

vector< CRef<CSeq_loc> >& q = aligner.

();

BOOST_REQUIRE_EQUAL(seqlocs.size(), q.size());

(

=0;

< q.size();

++) {

BOOST_CHECK(seqlocs[

]->

()->Match(*q[

]->

()));

vector< CRef<CSeq_loc> >& q = aligner.

();

BOOST_REQUIRE_EQUAL(bioseqs.size(), q.size());

(

=0;

< q.size();

++) {

BOOST_CHECK(bioseqs[

]->GetFirstId()->Match(*q[

]->

()));

BOOST_REQUIRE((*it)->GetId());

vector< CRef<CBioseq> > bioseqs;

s.

().SetId().Assign(

);

BOOST_REQUIRE(s.

());

vector< CRef<CSeq_loc> > seqlocs;

vector< CRef<CBioseq> > bioseqs;

seqlocs.push_back(m_Sequences.front());

BOOST_REQUIRE_EQUAL((

)seqlocs.size(), 1);

status =

(

, seqlocs, scope);

BOOST_REQUIRE_EQUAL(status, 0);

BOOST_CHECK_THROW(aligner.

(seqlocs, scope),

vector< CRef<CBioseq> > bioseqs;

m_Options->SetRpsDb(

);

query_index = (

)m_Sequences.size();

constr[0].seq1_index = query_index;

constr[0].seq1_start = 0;

constr[0].seq1_stop = 50;

constr[0].seq2_index = 0;

constr[0].seq2_start = 0;

constr[0].seq2_stop = 50;

BOOST_REQUIRE(m_Options->Validate());

BOOST_CHECK_THROW(m_Aligner->SetQueries(m_Sequences,

),

BOOST_CHECK_THROW(m_Aligner->SetQueries(bioseqs),

constr[0].seq1_index = 0;

constr[0].seq1_start = 0;

constr[0].seq1_stop = 50;

constr[0].seq2_index = 1;

constr[0].seq2_start = 0;

constr[0].seq2_stop = length + 1;

BOOST_REQUIRE(m_Options->Validate());

BOOST_CHECK_THROW(m_Aligner->SetQueries(m_Sequences,

),

BOOST_CHECK_THROW(m_Aligner->SetQueries(bioseqs),

m_Aligner->SetQueries(m_Sequences,

);

BOOST_CHECK(node->

().IsSetDist());

BOOST_CHECK(!node->

().GetLabel().empty());

BOOST_CHECK_EQUAL(node->

().GetId(),

= node->

().GetId();

BOOST_REQUIRE(!queries[

]);

BOOST_CHECK(node->

().GetLabel().empty());

vector<bool> used_queries(num_queries,

);

(vector<bool>, it, used_queries) {

vector<bool> used_queries(num_queries,

);

BOOST_CHECK((*it)->CanGetName());

((*it)->GetName() ==

) {

label_fid = (*it)->GetId();

((*it)->GetName() ==

) {

dist_fid = (*it)->GetId();

BOOST_REQUIRE(label_fid >= 0);

BOOST_REQUIRE(dist_fid >= 0);

((*node)->GetId() == 0) {

BOOST_REQUIRE((*node)->CanGetFeatures());

is_dist =

;

((*feat)->GetFeatureid() == label_fid) {

= (*feat)->GetValue();

* ptr =

.c_str();

BOOST_REQUIRE(!used_queries[

]);

used_queries[id] =

;

((*feat)->GetFeatureid() == dist_fid) {

BOOST_CHECK(is_dist);

(vector<bool>, it, used_queries) {

(clusters.empty()) {

vector<bool> used_queries(num_queries,

);

BOOST_REQUIRE(cluster->size() > 0);

num_elems += (

)cluster->size();

prototype = cluster->GetPrototype();

is_prototype =

;

BOOST_REQUIRE(!used_queries[*elem]);

used_queries[*elem] =

;

(prototype == *elem) {

is_prototype =

;

BOOST_CHECK(is_prototype);

BOOST_REQUIRE_EQUAL(num_elems, num_queries);

(vector<bool>, it, used_queries) {

(constraints.empty()) {

unordered_set<int> constr_queries;

constr_queries.insert(it->seq1_index);

constr_queries.insert(it->seq2_index);

remain = constr_queries.size();

unordered_set<int>::const_iterator it = constr_queries.find(*elem);

(it != constr_queries.end()) {

BOOST_CHECK_EQUAL(cluster->size(), 1u);

vector<CSequence>& seqs,

& aln_ref =

)

num_queries = (

)queries.size();

BOOST_REQUIRE_EQUAL(seqalign->

(), num_queries);

(

=0;

< num_queries;

++) {

BOOST_REQUIRE_EQUAL(seqs.size(), queries.size());

= seqs[0].GetLength();

(vector<CSequence>, it, seqs) {

BOOST_CHECK_EQUAL(it->GetLength(),

);

(

=0;

< queries.size();

++) {

num_residues = 0;

* sequence = seqs[

].GetSequence();

(

k=0;k < seqs[

].GetLength();k++) {

BOOST_CHECK_EQUAL(query_len, num_residues);

(!aln_ref.empty()) {

BOOST_REQUIRE_EQUAL(seqalign->

(), ref_align.

());

BOOST_REQUIRE_EQUAL(starts.size(), ref_starts.size());

BOOST_REQUIRE_EQUAL(lens.size(), ref_lens.size());

(

=0;

< starts.size();

++) {

BOOST_CHECK_EQUAL(starts[

], ref_starts[

]);

(

=0;

< lens.size();

++) {

BOOST_CHECK_EQUAL(lens[

], ref_lens[

]);

& ref_aln =

)

kNumQueries = (

)aligner.

().size();

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

BOOST_CHECK_EQUAL((

)m_Aligner->GetMessages().size(), 0);

m_Options->SetMaxInClusterDist(0.0);

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

BOOST_CHECK((

)m_Aligner->GetMessages().size() == 0);

m_Options->SetMaxInClusterDist(1.0);

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

BOOST_CHECK_EQUAL((

)m_Aligner->GetMessages().size(), 0);

vector<CMultiAlignerOptions::SConstraint>& constr

= m_Options->SetUserConstraints();

constr[0].seq1_index = 0;

constr[0].seq1_start = 0;

constr[0].seq1_stop = 50;

constr[0].seq2_index = 1;

constr[0].seq2_start = 0;

constr[0].seq2_stop = 50;

constr[1].seq1_index = 1;

constr[1].seq1_start = 0;

constr[1].seq1_stop = 50;

constr[1].seq2_index = 5;

constr[1].seq2_start = 0;

constr[1].seq2_stop = 50;

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

BOOST_CHECK_EQUAL((

)m_Aligner->GetMessages().size(), 0);

m_Options->SetMaxInClusterDist(1.0);

vector< CRef<CSeq_loc> > queries;

queries.push_back(m_Sequences[0]);

queries.push_back(m_Sequences[1]);

m_Aligner->SetQueries(queries,

);

m_Options->SetMaxInClusterDist(0.01);

m_Aligner->SetQueries(queries,

);

status = m_Aligner->Run();

vector< CRef<CSeq_loc> > sequences;

BOOST_REQUIRE_EQUAL(

(

, sequences, scope,

m_Options->SetUseQueryClusters(

);

BOOST_REQUIRE(

->GetSegs().IsDenseg());

num_input_sequences = (

)first_denseg.

()

+ second_denseg.

();

BOOST_REQUIRE_EQUAL(

->GetDim(), num_input_sequences);

vector<int> first_rows, second_rows;

(

=0;

< first_denseg.

().

();

++) {

(;j <

->GetDim();j++) {

(

.Match(*

->GetSegs().GetDenseg().GetIds()[j])) {

first_rows.push_back(j);

BOOST_REQUIRE(j < result->GetDim());

(

=0;

< second_denseg.

().

();

++) {

(;j <

->GetDim();j++) {

(

.Match(*

->GetSegs().GetDenseg().GetIds()[j])) {

second_rows.push_back(j);

BOOST_REQUIRE(j < result->GetDim());

->RemovePureGapSegs();

BOOST_REQUIRE_EQUAL(first_denseg.

().size(),

->GetStarts().size());

BOOST_REQUIRE_EQUAL(first_denseg.

().size(),

->GetLens().size());

BOOST_REQUIRE_EQUAL(first_denseg.

()[

],

->GetStarts()[

]);

(

=0;

< first_denseg.

().

();

++) {

BOOST_REQUIRE_EQUAL(first_denseg.

()[

],

->GetLens()[

]);

BOOST_REQUIRE_EQUAL(second_denseg.

().size(), s->

().size());

(

=0;

< second_denseg.

().

();

++) {

m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

);

*

(m_Sequences.front()->GetId())));

m_Aligner->SetInputMSAs(*m_Align1, *align, repr, repr,

);

BOOST_REQUIRE(m_Align1->CheckNumRows() > 3);

BOOST_REQUIRE(m_Align2->CheckNumRows() > 3);

m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

);

BOOST_CHECK_THROW(m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

repr.

(m_Align1->CheckNumRows());

BOOST_CHECK_THROW(m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

vector< CRef<CSeq_id> > expected_queries;

= (*it)->GetId()->AsFastaString();

m_Options->SetUseQueryClusters(

);

m_Options->SetRpsEvalue(0.1);

m_Aligner->SetQueries(m_Sequences,

);

BOOST_REQUIRE_EQUAL(m_Options->GetUseQueryClusters(),

);

BOOST_REQUIRE(

(m_Options->GetRpsEvalue() - 0.1) < 0.01);

BOOST_REQUIRE_EQUAL(expected_queries.size(),

m_Aligner->GetQueries().size());

(

=0;

< expected_queries.size();

++) {

BOOST_REQUIRE(expected_queries[

]->CompareOrdered(

*m_Aligner->GetQueries()[

]->GetId()) == 0);

vector<bool> expected_is_domain_searched(m_Sequences.size(),

);

expected_is_domain_searched[0] =

;

expected_is_domain_searched[2] =

;

BOOST_REQUIRE_EQUAL(expected_is_domain_searched.size(),

(

=0;

< expected_is_domain_searched.size();

++) {

BOOST_REQUIRE_EQUAL(expected_is_domain_searched[

],

kNumExpectedPreHits = 7;

vector<SHit> expected_hits(kNumExpectedPreHits);

expected_hits[0].query =

;

expected_hits[0].subject = 1;

expected_hits[0].query_range =

(6, 382);

expected_hits[0].subject_range =

(0, 372);

expected_hits[0].score = 1414;

expected_hits[1].query =

;

expected_hits[1].subject = 0;

expected_hits[1].query_range =

(95, 377);

expected_hits[1].subject_range =

(42, 325);

expected_hits[1].score = 885;

expected_hits[2].query =

;

expected_hits[2].subject = 2;

expected_hits[2].query_range =

(1, 382);

expected_hits[2].subject_range =

(19, 405);

expected_hits[2].score = 718;

expected_hits[3].query =

;

expected_hits[3].subject = 2;

expected_hits[3].query_range =

(41, 448);

expected_hits[3].subject_range =

(0, 408);

expected_hits[3].score = 1779;

expected_hits[4].query =

;

expected_hits[4].subject = 1;

expected_hits[4].query_range =

(88, 440);

expected_hits[4].subject_range =

(22, 367);

expected_hits[4].score = 981;

expected_hits[5].query =

;

expected_hits[5].subject = 0;

expected_hits[5].query_range =

(151, 440);

expected_hits[5].subject_range =

(42, 325);

expected_hits[5].score = 872;

expected_hits[6].query =

;

expected_hits[6].subject = 0;

expected_hits[6].query_range =

(511, 581);

expected_hits[6].subject_range =

(208, 280);

expected_hits[6].score = 75;

BOOST_REQUIRE_MESSAGE(hits_match, errors);

m_Aligner->SetInterruptCallback(

kNumExpectedHits = 10;

BOOST_REQUIRE(kNumExpectedHits > kNumExpectedPreHits);

expected_hits.resize(kNumExpectedHits);

expected_hits[7].query =

;

expected_hits[7].subject = 2;

expected_hits[7].query_range =

(27, 432);

expected_hits[7].subject_range =

(0, 400);

expected_hits[7].score = 768;

expected_hits[8].query =

;

expected_hits[8].subject = 0;

expected_hits[8].query_range =

(138, 433);

expected_hits[8].subject_range =

(42, 326);

expected_hits[8].score = 738;

expected_hits[9].query =

;

expected_hits[9].subject = 1;

expected_hits[9].query_range =

(75, 434);

expected_hits[9].subject_range =

(24, 369);

expected_hits[9].score = 704;

BOOST_REQUIRE_MESSAGE(hits_match, errors);

vector< CRef<CSeq_id> > expected_queries;

= (*it)->GetId()->AsFastaString();

m_Options->SetUseQueryClusters(

);

m_Options->SetRpsEvalue(0.1);

m_Aligner->SetQueries(m_Sequences,

);

BOOST_REQUIRE_EQUAL(m_Options->GetUseQueryClusters(),

);

BOOST_REQUIRE(

(m_Options->GetRpsEvalue() - 0.1) < 0.01);

BOOST_REQUIRE_EQUAL(expected_queries.size(),

m_Aligner->GetQueries().size());

(

=0;

< expected_queries.size();

++) {

BOOST_REQUIRE(expected_queries[

]->CompareOrdered(

*m_Aligner->GetQueries()[

]->GetId()) == 0);

vector<bool> expected_is_domain_searched(m_Sequences.size(),

);

expected_is_domain_searched[0] =

;

expected_is_domain_searched[2] =

;

BOOST_REQUIRE_EQUAL(expected_is_domain_searched.size(),

(

=0;

< expected_is_domain_searched.size();

++) {

BOOST_REQUIRE_EQUAL(expected_is_domain_searched[

],

kNumExpectedPreHits = 7;

vector<SHit> expected_hits(kNumExpectedPreHits);

expected_hits[0].query =

;

expected_hits[0].subject = 1;

expected_hits[0].query_range =

(6, 382);

expected_hits[0].subject_range =

(0, 372);

expected_hits[0].score = 1414;

expected_hits[1].query =

;

expected_hits[1].subject = 0;

expected_hits[1].query_range =

(95, 377);

expected_hits[1].subject_range =

(42, 325);

expected_hits[1].score = 885;

expected_hits[2].query =

;

expected_hits[2].subject = 2;

expected_hits[2].query_range =

(1, 382);

expected_hits[2].subject_range =

(19, 405);

expected_hits[2].score = 718;

expected_hits[3].query =

;

expected_hits[3].subject = 2;

expected_hits[3].query_range =

(41, 448);

expected_hits[3].subject_range =

(0, 408);

expected_hits[3].score = 1779;

expected_hits[4].query =

;

expected_hits[4].subject = 1;

expected_hits[4].query_range =

(88, 440);

expected_hits[4].subject_range =

(22, 367);

expected_hits[4].score = 981;

expected_hits[5].query =

;

expected_hits[5].subject = 0;

expected_hits[5].query_range =

(151, 440);

expected_hits[5].subject_range =

(42, 325);

expected_hits[5].score = 872;

expected_hits[6].query =

;

expected_hits[6].subject = 0;

expected_hits[6].query_range =

(511, 581);

expected_hits[6].subject_range =

(208, 280);

expected_hits[6].score = 75;

BOOST_REQUIRE_MESSAGE(hits_match, errors);

m_Aligner->SetInterruptCallback(

kNumExpectedHits = 10;

BOOST_REQUIRE(kNumExpectedHits > kNumExpectedPreHits);

expected_hits.resize(kNumExpectedHits);

expected_hits[7].query =

;

expected_hits[7].subject = 2;

expected_hits[7].query_range =

(27, 432);

expected_hits[7].subject_range =

(0, 400);

expected_hits[7].score = 768;

expected_hits[8].query =

;

expected_hits[8].subject = 0;

expected_hits[8].query_range =

(138, 433);

expected_hits[8].subject_range =

(42, 326);

expected_hits[8].score = 738;

expected_hits[9].query =

;

expected_hits[9].subject = 1;

expected_hits[9].query_range =

(75, 434);

expected_hits[9].subject_range =

(24, 369);

expected_hits[9].score = 704;

BOOST_REQUIRE_MESSAGE(hits_match, errors);

m_Options->SetUseQueryClusters(

);

vector< CRef<CSeq_loc> > queries;

queries.push_back(m_Sequences.back());

queries.push_back(m_Sequences.back());

m_Aligner->SetQueries(queries,

);

vector< CRef<CSeq_loc> > queries;

seq->

().Set(

);

queries.push_back(seq);

queries.push_back(seq);

m_Options->SetRpsEvalue(10);

m_Options->SetUseQueryClusters(

);

m_Aligner->SetQueries(queries,

);

m_Options->SetRpsEvalue(0.00001);

m_Aligner->SetQueries(queries,

);

BOOST_REQUIRE_EQUAL(

m_Options->SetUseQueryClusters(

);

m_Options->SetDomainHits(m_RpsArchive);

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetQueries(m_Sequences,

);

m_Options->SetUseQueryClusters(

);

BOOST_REQUIRE(m_Options->CanGetDomainHits());

m_Aligner->SetQueries(m_Sequences,

);

m_Options->SetRpsEvalue(10);

m_Options->SetDomainHits(m_RpsArchive);

BOOST_REQUIRE(m_Options->Validate());

m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

);

BOOST_REQUIRE(m_Options->CanGetDomainHits());

m_Aligner->SetInputMSAs(*m_Align1, *m_Align2, repr, repr,

);

m_Options->SetUseQueryClusters(

);

m_Aligner->SetQueries(m_Sequences,

);

istr(

);

BOOST_REQUIRE(istr);

(

)

);

(

)

);

m_Options->SetUseQueryClusters(

);

m_Aligner->SetQueries(m_Sequences,

);

& pssm = m_RpsArchive->SetRequest().SetBody().SetQueue_search()

.SetQueries().SetPssm().SetPssm();

static CRef< CScope > m_Scope

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

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

vector< TSingleCluster > TClusters

void RemovePureGapSegs()

Remove any segments in which every row has a gap (these can arise when ExtractRows is used)

void Compact()

Join adjacent mergeable segments to create a more compact alignment.

An ordered collection of CHit objects.

int Size() const

Retrieve number of hits in list.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

A generalized representation of a pairwise alignment.

int m_Score

Score of alignment.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

TRange m_SeqRange2

The range of offsets on the second sequence.

Fixture class initialized for each multialigner test.

static CRef< CBlast4_archive > m_RpsArchive

static CRef< CObjectManager > m_Objmgr

static void Initialize(void)

Initialize static attributes.

static CRef< CScope > m_Scope

CRef< CMultiAlignerOptions > m_Options

static vector< CRef< CSeq_loc > > m_Sequences

static void x_ReadSequences(void)

Read test sequences in FASTA format from file.

static void x_InitScope(void)

Initialize scope.

static void x_ReadAlignments(void)

Read test MSAs from files.

static void x_ReadRpsArchive(void)

Read test RPS-BLAST output in the archive format from file.

CMultiAlignerFixture(void)

static CRef< CSeq_align > m_Align2

CRef< CMultiAligner > m_Aligner

static void Finalize(void)

Release static attributes.

static CRef< CSeq_align > m_Align1

Options and parameters for multiple alignement.

void SetRpsDb(const string &dbname)

Use RPS Blast with given database.

const TConstraints & GetUserConstraints(void) const

Get user constraints.

@ fNoQueryClusters

No query clustering.

@ fNoRpsBlast

Do not use RPS Blast.

vector< SConstraint > TConstraints

Test class for accessing CMultiAligner private attributes and methods.

static void SetDomainHits(CMultiAligner &aligner, CConstRef< CBlast4_archive > archive)

Set pre-computed domain hits without invoking CMlultiAligner::Run()

static bool InterruptAfterRpsBlastSearch(CMultiAligner::SProgress *progress)

Quit after doing RPS-BLAST search.

static void SetQuerySeqlocs(CMultiAligner &aligner, const vector< CRef< CSeq_loc > > &queries)

Set queries in the aligner only as Seq-locs do not retrieve sequences.

static const vector< bool > & GetIsDomainSearched(const CMultiAligner &aligner)

static const CHitList & GetDomainHits(const CMultiAligner &aligner)

static bool CompareDomainHits(const vector< SHit > &expected_hits, const CMultiAligner &aligner, string &err)

Compare domain hits in CMultiAligner with reference alignements.

Simultaneously align multiple protein sequences.

CConstRef< CMultiAlignerOptions > GetOptions(void) const

Get mutli aligner parameters.

const vector< CSequence > & GetSeqResults(void) const

Retrieve the current aligned results in CSequence format.

const vector< CRef< objects::CSeq_loc > > & GetQueries(void) const

Get query sequences.

CRef< objects::CSeq_align > GetResults(void) const

Retrieve the current aligned results in Seq-align format.

vector< CRef< objects::CSeq_loc > > m_tQueries

TStatus Run(void)

Align the current set of input sequences (reset any existing alignment information).

const TPhyTreeNode * GetTree(void) const

Get ree used guide in progressive alignment.

@ eOutOfMemory

Out of memory error.

@ eSuccess

Alignment successfully completed.

@ eInterrupt

Alignment interruped through callback function.

const CClusterer::TClusters & GetQueryClusters(void) const

Get clusters of query sequences.

vector< bool > m_IsDomainSearched

Marks sequences with pre-computed domain hits.

void SetQueries(const vector< CRef< objects::CSeq_loc > > &queries, CRef< objects::CScope > scope)

Set query sequences.

CRef< objects::CScope > GetScope(void)

Get scope.

void x_SetDomainHits(const blast::TSeqLocVector &queruies, const vector< int > &indices, const objects::CBlast4_archive &archive)

Set pre-computed domain hits using BLAST archive format.

CRef< objects::CBioTreeContainer > GetTreeContainer(void) const

Get serializable tree used as guide in progressive alignment.

void x_CreateBlastQueries(blast::TSeqLocVector &queries, vector< int > &indices)

Create query set for RPS Blast and Blastp searches along with indices in multiple alignment queries a...

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

static const unsigned char kGapChar

The ncbistdaa code for a gap.

definition of a Culling tree

iterator_bool insert(const value_type &val)

Interface for CMultiAligner.

int ReadFastaQueries(const string &filename, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator)

int ReadMsa(const string &filename, CRef< CSeq_align > &align, CRef< CScope > scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator)

static void s_TestResultAlignment(const vector< CRef< CSeq_loc > > &queries, const CRef< CSeq_align > &seqalign, const vector< CSequence > &seqs, CRef< CScope > scope, const string &aln_ref="")

static void s_TestResultTreeContainer(int num_queries, const CBioTreeContainer &btc)

static void s_TestResults(CMultiAligner &aligner, const string &ref_aln="")

BOOST_AUTO_TEST_CASE(TestSetQueries)

static bool s_Interrupt(CMultiAligner::SProgress *progress)

static void s_MakeBioseqs(const vector< CRef< CSeq_loc > > &seqlocs, CRef< CScope > scope, vector< CRef< CBioseq > > &bioseqs)

void s_TestAlignmentFromMSAs(CRef< CSeq_align > result, CRef< CSeq_align > in_first, CRef< CSeq_align > in_second)

static void s_TestResultTree(int num_queries, const TPhyTreeNode *tree)

static void s_TestQueriesAsBioseqs(const vector< CRef< CBioseq > > &bioseqs)

static void s_TestQueriesAsSeq_locs(const vector< CRef< CSeq_loc > > &seqlocs, CRef< CScope > scope)

static void s_TestResultClusters(int num_queries, const CClusterer::TClusters &clusters, const CMultiAlignerOptions::TConstraints &constraints)

static void s_TestTree(vector< bool > &queries, const TPhyTreeNode *node)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define MSerial_AsnText

I/O stream manipulators –.

const string AsFastaString(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

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.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Convert int to string.

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

Convert UInt to string.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList::const_iterator TNodeList_CI

bool IsLeaf() const

Report whether this is a leaf node.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

const TValue & GetValue(void) const

Return node's value.

const TTreeType * GetParent(void) const

Get node's parent.

static const char label[]

list< CRef< CFeatureDescr > > Tdata

list< CRef< CNodeFeature > > Tdata

list< CRef< CNode > > Tdata

const Tdata & Get(void) const

Get the member data.

const Tdata & Get(void) const

Get the member data.

const TFdict & GetFdict(void) const

Get the Fdict member data.

const TNodes & GetNodes(void) const

Get the Nodes member data.

const TAlignments & GetAlignments(void) const

Get the Alignments member data.

const TResults & GetResults(void) const

Get the Results member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetNumColumns(TNumColumns value)

Assign a value to NumColumns data member.

void SetNumRows(TNumRows value)

Assign a value to NumRows data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

TDim GetDim(void) const

Get the Dim member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

void SetDim(TDim value)

Assign a value to Dim data member.

vector< TSignedSeqPos > TStarts

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TType GetType(void) const

Get the Type member data.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

unsigned int

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

const struct ncbi::grid::netcache::search::fields::SIZE size

Options for CMultiAligner.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure for reporting alignment progress.

Representation of a hit for computing constraints.

int subject

subject ordinal id in the database

TRange query_range

alignment extents

int score

alignment score

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

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