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NCBI C++ ToolKit: src/algo/sequence/unit_test/unit_test_gap_analysis.cpp Source File

57 const string

& summary_name,

58

GA::EGapType eGapType,

59 const

GA::TVectorGapLengthSummary & summary )

61

cerr <<

"BEGIN "

<< GA::s_GapTypeToStr(eGapType)

62

" SUMMARY for "

<< summary_name << endl;

63 ITERATE

( GA::TVectorGapLengthSummary, summary_iter,

66 const

GA::SOneGapLengthSummary & one_summary =

68

cerr <<

"\tlen: "

<< one_summary.gap_length

69

"\tnum seqs: "

<< one_summary.num_seqs

70

"\tnum gaps: "

<< one_summary.num_gaps << endl;

72

cerr <<

"END GAP SUMMARY"

<< endl;

75 void

s_PrintSummaryForAllGapTypes(

76 const string

& summary_name,

80

cout <<

"GAP SUMMARY FOR ALL GAP_TYPES"

<< endl;

82

GA::EGapType gap_types[] = {

84

GA::eGapType_UnknownBases

87

GA::EGapType eGapType = gap_types[gap_idx];

108

s_scope->AddDefaults();

112 void

LoadSeqEntryIntoGapAnalysis(

115

GA::TAddFlag add_flags,

116

GA::TFlag fFlags = 0,

118 bool

do_rev_comp =

false

)

123

: CreateScope().GetPointer() );

129 if

( entry->IsSeq() ) {

131

entry->SetSeq().SetInst(), scope.GetPointer());

137

scope->AddTopLevelSeqEntry(*pSeqEntry);

138

BOOST_REQUIRE( entry_h );

150

GA::TAddFlag add_flags = GA::fAddFlag_All,

151

GA::EGapType gap_type = GA::eGapType_All,

152

GA::TFlag fFlags = 0)

154

in_text_asn.seekg(0);

160

LoadSeqEntryIntoGapAnalysis(

161

gap_analysis, pSeqEntry, add_flags, fFlags);

166 struct

SExpectedResult {

171 bool empty

(

void

)

const

{

173 return

0 == (

gap_length

| num_seqs | num_gaps); }

176 static const

SExpectedResult s_ExpectedResultEnd = {0, 0, 0};

179

ostream& s,

const

SExpectedResult & expected_result)

181

s <<

"SExpectedResult (" 182

"gap_length: "

<< expected_result.gap_length

183

", num_seqs: "

<< expected_result.num_seqs

184

", num_gaps: "

<< expected_result.num_gaps <<

")"

;

189

ostream& s,

const

SExpectedResult expected_results[] )

191

s <<

"The expected results: ("

<< endl;

193 for

(

size_t

idx = 0; ! expected_results[idx].empty(); ++idx ) {

194 const

SExpectedResult & one_expected_result =

195

expected_results[idx];

196

s << one_expected_result << endl;

203 void

CheckExpectedResults(

204 const

GA::TVectorGapLengthSummary & basic_gap_summary,

207 const

SExpectedResult expected_results[])

209

cout <<

"CheckExpectedResults basic_gap_summary: " 210

<< basic_gap_summary << endl;

213 for

( ; idx < basic_gap_summary.size(); ++idx) {

214 const

GA::SOneGapLengthSummary & one_gap_summary =

215

*basic_gap_summary[idx];

216 const

SExpectedResult & one_expected_result =

217

expected_results[idx];

219

one_gap_summary.gap_length, one_expected_result.gap_length);

221

one_gap_summary.num_seqs, one_expected_result.num_seqs);

223

one_gap_summary.num_gaps, one_expected_result.num_gaps);

225

BOOST_CHECK( expected_results[idx].

empty

() );

229 struct

SGapTypeExpectedResult {

230 const

GA::EGapType gap_type;

233 const

SExpectedResult expected_result[5];

236 void

CheckGapTypeExpectedResult(

238 const

SGapTypeExpectedResult & gap_type_expected_result,

239 const

GA::TVectorGapLengthSummary & basic_gap_summary)

241

cout <<

"In "

test_name

" running expected results for " 242

<< GA::s_GapTypeToStr(gap_type_expected_result.gap_type) <<

": " 243

<< gap_type_expected_result.expected_result << endl;

245

CheckExpectedResults(

247

gap_type_expected_result.expected_result);

256

arg_desc->AddKey(

"basic-data"

"InputFile"

257 "This is the basic input file used to run the test"

260 "in-letter-gap-data"

"InputFile"

261 "This is the input file used to run the " 262 "'gaps as run of unknown bases' test"

265 "mixed-gap-type-data"

"InputFile"

266 "This is the input file used to run the " 267 "'gaps as run of unknown bases and seq-gaps' test, distinguishing " 277 CNcbiIfstream

basic_data_fstrm(args[

"basic-data"

].AsString().c_str());

279

AnalyzeSeqEntryTextAsn(

280

basic_data_fstrm, GA::fAddFlag_All, GA::eGapType_All,

281

GA::fFlag_IncludeEndGaps);

283 "TestBasic - basic-data"

, GA::eGapType_All, *basic_gap_summary);

285

SExpectedResult expected_results[] = {

292

CheckExpectedResults(*basic_gap_summary, expected_results);

303 const

GA::TGapLength kGapLength = 10;

304 const TSeqPos

kBioseqlen = 100;

308

GA::eGapType_All, pSeqId1, kGapLength, kBioseqlen, 2, 12);

310

GA::eGapType_All, pSeqId2, kGapLength, kBioseqlen, 20, 30);

312

GA::eGapType_All, pSeqId3, kGapLength, kBioseqlen, 40, 50);

316

kGapLength)->second.size(),

324 CNcbiIfstream

gap_data_strm(args[

"in-letter-gap-data"

].AsString().c_str());

326

AnalyzeSeqEntryTextAsn(

327

gap_data_strm, GA::fAddFlag_IncludeUnknownBases,

328

GA::eGapType_All, GA::fFlag_IncludeEndGaps);

330 "TestGapsAsLetters - in-letter-gap-data"

331

GA::eGapType_All, *basic_gap_summary);

333

SExpectedResult expected_results[] = {

339

CheckExpectedResults(*basic_gap_summary, expected_results);

347

args[

"mixed-gap-type-data"

].AsString().c_str());

352

LoadSeqEntryIntoGapAnalysis(

353

gap_analysis, pSeqEntry, GA::fAddFlag_All,

354

GA::fFlag_IncludeEndGaps);

355

s_PrintSummaryForAllGapTypes(

356 "TestEndGaps - mixed-gap-type-data"

, gap_analysis);

358 const

SGapTypeExpectedResult gap_type_expected_results[] = {

376

GA::eGapType_UnknownBases,

388

CheckGapTypeExpectedResult(

390

gap_type_expected_results[gap_type_idx],

392

gap_type_expected_results[gap_type_idx].gap_type));

403 const

SGapTypeExpectedResult gap_type_expected_results[] = {

419

GA::eGapType_UnknownBases,

431

cout <<

"TestAllGapTypes " 432

<< (is_minus_strand ?

"minus"

"plus"

)

433

" strand"

<< endl;

436

args[

"mixed-gap-type-data"

].AsString().c_str());

441

LoadSeqEntryIntoGapAnalysis(

443

gap_analysis, pSeqEntry, GA::fAddFlag_All, 0,

NULL

true

);

444

s_PrintSummaryForAllGapTypes(

445 "TestAllGapTypes - mixed-gap-type-data"

, gap_analysis);

449 const

SGapTypeExpectedResult & gap_type_expected_result =

450

gap_type_expected_results[gap_type_idx];

452

CheckGapTypeExpectedResult(

454

gap_type_expected_result,

456

gap_type_expected_result.gap_type));

467

cout <<

"(NULL)"

<< endl;

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Give this gaps, or handles containing gaps and then you can get statistics on those gaps.

const TMapGapLengthToSeqIds & GetGapLengthSeqIds(EGapType eGapType) const

Returns a map of gap_length to the set of all seq-ids that contain at least one gap of that length.

void AddSeqEntryGaps(const CSeq_entry_Handle &entry_h, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set, CBioseq_CI::EBioseqLevelFlag level=CBioseq_CI::eLevel_All, TAddFlag add_flags=fAddFlag_All, TFlag fFlags=0, size_t max_resolve_count=kMax_Int)

Calls AddGap for each gap anywhere under the given CSeq_entry.

void AddGap(EGapType eGapType, TSeqIdConstRef pSeqId, TGapLength iGapLength, TSeqPos iBioseqLength, TSeqPos iGapStartPos, TSeqPos iGapEndPosExclusive, TFlag fFlags=0)

AddSeqEntryGaps is more convenient, but if you want finer-grained control you can use this function t...

AutoPtr< TVectorGapLengthSummary > GetGapLengthSummary(EGapType eGapType, ESortGapLength eSortGapLength=eSortGapLength_Length, ESortDir eSortDir=eSortDir_Ascending) const

This gives summary information about every gap-length encountered so far.

static CNcbiApplication * Instance(void)

Singleton method.

Base class for all serializable objects.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Template class for iteration on objects of class C.

const_iterator find(const key_type &key) const

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

static char test_name[128]

Analyzes gaps and produces various statistics.

void ReverseComplement(const BidirectionalIterator &first, const BidirectionalIterator &last)

#define ITERATE_0_IDX(idx, up_to)

idx loops from 0 (inclusive) to up_to (exclusive)

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ITERATE_BOTH_BOOL_VALUES(BoolVar)

The body of the loop will be run with Var equal to false and then true.

@ eInputFile

Name of file (must exist and be readable)

#define MSerial_AsnText

I/O stream manipulators â.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void Reset(void)

Reset reference object.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

@ eMol_not_set

> cdna = rna

bm::gap_word_t gap_length(const bm::gap_word_t *buf) noexcept

Returs GAP block length.

constexpr bool empty(list< Ts... >) noexcept

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

CRef< objects::CObjectManager > om

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

BOOST_AUTO_TEST_CASE(TestBasic)

NCBITEST_INIT_CMDLINE(arg_desc)

void PS(const CSerialObject *obj)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unit__test__gap__analysis_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/sequence/unit_test/unit_test_gap_analysis.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestgap__analysis_8cpp_source.html below: