RetroSearch Browse

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestsplign_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/splign/unit_test/unit_test_splign.cpp Source File

66

arg_desc->AddOptionalKey(

"mrna-data-in"

"mrna_data_in"

67 "Concatenated CSeq_annots (blast results) used to run splign with mrna parameter set"

70

arg_desc->AddOptionalKey(

"mrna-expected"

"mrna_data_out"

71 "Expected output for mrna parameter set (concatenatd CSeq_align_sets)."

76

arg_desc->AddOptionalKey(

"mrna-out"

"mrna_out"

"output alignment file"

82

arg_desc->AddDefaultKey(

"mrna-outfmt"

"mrna_output_format"

"output format for file specified with -mrna-out"

CArgDescriptions::eString

"splign"

);

88

arg_desc->SetConstraint(

"mrna-outfmt"

, cons);

92

arg_desc->AddOptionalKey(

"est-data-in"

"est_data_in"

93 "Concatenated CSeq_annots (blast results) used to run splign with est parameter set"

96

arg_desc->AddOptionalKey(

"est-expected"

"est_data_out"

97 "Expected output for est parameter set (concatenatd CSeq_align_sets)."

102

arg_desc->AddOptionalKey(

"est-out"

"est_out"

"output alignment file"

108

arg_desc->AddDefaultKey(

"est-outfmt"

"est_output_format"

"output format for file specified with -est-out"

CArgDescriptions::eString

"splign"

);

112

arg_desc->SetConstraint(

"est-outfmt"

, cons);

118 if

(align->

IsSet

()) {

120

BOOST_CHECK( (*sait)->GetSegs().IsSpliced() );

121 if

( (*sait)->SetSegs().SetSpliced().IsSetExons() ) {

123 if

( (*exot)->IsSetScores() && (*exot)->SetScores().IsSet() ) {

125 if

( (*sit)->IsSetValue() && (*sit)->SetValue().IsReal() ) {

128

ots1 << setprecision(7) << scientific << re;

132

(*sit)->SetValue().SetReal(re);

148 if

(args[

"mrna-data-in"

] || args[

"est-data-in"

]) {

179 if

(args[

"mrna-data-in"

]) {

184 CNcbiIstream

& istr = args[

"mrna-data-in"

].AsInputFile();

187 if

(args[

"mrna-out"

]) {

188

ofmt = args[

"mrna-outfmt"

].AsString();

203

TAllHits one_seq_annot_hits_in;

213

one_seq_annot_hits_in[make_pair(idh1, idh2)].push_back(tr);

231

sf.

SetSeqIds

(qsit->first.first.GetSeqId(), qsit->first.second.GetSeqId());

232

splign.

Run

(&(qsit->second));

234

splign_out->

Set

().insert(splign_out->

Set

().end(), sas->

Get

().begin(), sas->

Get

().end());

235 if

(args[

"mrna-out"

]) {

236 if

(ofmt ==

"text"

) {

237 CNcbiOstream

& ostr = args[

"mrna-out"

].AsOutputFile();

238

ostr<<sf. AsAlignmentText(scope, &splign.

GetResult

())<<endl;

239

}

else if

(ofmt ==

"splign"

) {

240 CNcbiOstream

& ostr = args[

"mrna-out"

].AsOutputFile();

245 if

(args[

"mrna-out"

] && ofmt ==

"asn"

) {

246 CNcbiOstream

& ostr = args[

"mrna-out"

].AsOutputFile();

252 if

(args[

"mrna-expected"

]) {

253 CNcbiIstream

& estr = args[

"mrna-expected"

].AsInputFile();

256

*es >> *expected_out;

272

BOOST_CHECK ( splign_out->

Equals

(*expected_out) );

291 if

(args[

"est-data-in"

]) {

297 CNcbiIstream

& istr = args[

"est-data-in"

].AsInputFile();

300 if

(args[

"est-out"

]) {

301

ofmt = args[

"est-outfmt"

].AsString();

316

TAllHits one_seq_annot_hits_in;

326

one_seq_annot_hits_in[make_pair(idh1, idh2)].push_back(tr);

332

sf.

SetSeqIds

(qsit->first.first.GetSeqId(), qsit->first.second.GetSeqId());

333

splign.

Run

(&(qsit->second));

335

splign_out->

Set

().insert(splign_out->

Set

().end(), sas->

Get

().begin(), sas->

Get

().end());

336 if

(args[

"est-out"

]) {

337 if

(ofmt ==

"text"

) {

339

ostr<<sf. AsAlignmentText(scope, &splign.

GetResult

())<<endl;

340

}

else if

(ofmt ==

"splign"

) {

346 if

(args[

"est-out"

] && ofmt ==

"asn"

) {

353 if

(args[

"est-expected"

]) {

354 CNcbiIstream

& estr = args[

"est-expected"

].AsInputFile();

357

*es >> *expected_out;

361

BOOST_CHECK ( splign_out->

Equals

(*expected_out) );

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

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CRef< objects::CSeq_align_set > AsSeqAlignSet(const CSplign::TResults *results=0, int flags=eAF_SplicedSegWithParts) const

Format alignment as a seq-align-set.

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

string AsExonTable(const CSplign::TResults *results=0, int flags=eTF_None) const

@ eAF_SplicedSegWithParts

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

void Run(THitRefs *hitrefs)

void SetCompartmentPenalty(double penalty)

void SetMinSingletonIdentity(double idty)

CRef< objects::CScope > & SetScope(void)

void SetMinPolyaLen(size_t len)

void SetMaxIntron(size_t max_intron)

void SetMinSingletonIdentityBps(size_t idty)

void SetMinExonIdentity(double idty)

void PreserveScope(bool preserve=true)

Controls whether to clean the scope object's cache on a new sequence.

const TResults & GetResult(void) const

void SetScoringType(EScoringType type)

void SetStartModelId(size_t model_id)

vector< THitRef > THitRefs

void SetAlignerScores(void)

void SetPolyaExtIdentity(double idty)

CRef< TAligner > & SetAligner(void)

Access the spliced aligner core object.

void SetMinCompartmentIdentity(double idty)

static CRef< CSplicedAligner > s_CreateDefaultAligner(void)

void SetSpaceLimit(const size_t &maxmem)

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eRequires

One argument requires another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

#define MSerial_AsnText

I/O stream manipulators â.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

@ eSerial_AsnText

ASN.1 text.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

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

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CScore > > Tdata

list< CRef< CSpliced_exon > > TExons

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

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(TestUsingArg)

void s_RoundScores(CRef< CSeq_align_set > align)

NCBITEST_INIT_CMDLINE(arg_desc)

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

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

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

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unit__test__splign_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/splign/unit_test/unit_test_splign.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestsplign_8cpp_source.html below: