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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bsdiff_8cpp_source.html below:

NCBI C++ ToolKit: src/app/bsdiff/bsdiff.cpp Source File

112 using namespace ncbi

;

114 using namespace xml

;

115 using namespace

biosample_util;

133 const string

& bioSampleAcc)

137

bioSampleAcc,

false

nullptr

);

151 for

(

auto

pSourceDesc: pDescriptorSet.

Get

()) {

152 const CSeqdesc

& sourceDesc = *pSourceDesc;

157

bioSample, sourceDesc.

GetSource

(), diffs);

165 const string

& fileName)

168

unique_ptr<CNcbiIfstream> pInStr(

new CNcbiIfstream

(fileName.c_str(), ios::binary));

184 const string

& bioSampleAcc,

190

cerr <<

"Differ: Unable to load biosample with given accession."

"\n"

;

201 const string

& bioSampleAcc,

210

bioSampleAcc, bioSource, sampleSource, diffs)) {

219 const string

& bioSampleFile,

234 const string

& inFile)

237

unique_ptr<CNcbiIfstream> pInStr(

new CNcbiIfstream

(inFile.c_str(), ios::binary));

258 virtual void Init

(

void

);

259 virtual int Run

(

void

);

262 int

xCompareSeqEntry(

264 int

xCompareSeqEntryAccession(

266 int

xCompareSeqEntryAccessionList(

268 int

xCompareSeqEntryFile(

276

vector<string> xGetBioSampleAccs(

294

mpScope.Reset(

new CScope

(*mpObjmgr));

295

mpScope->AddDefaults();

305

arg_desc->AddDefaultKey(

308 "BioSource info to compare"

312

arg_desc->AddDefaultKey(

314 "biosample_accession"

315 "biosample, retrieve online by accession"

319

arg_desc->AddDefaultKey(

321 "biosample_local_filename"

322 "biosample, retrieve locally from filename"

326

arg_desc->AddDefaultKey(

328 "seq_entry_accession"

329 "seq-entry, to be used for both biosource and biosample"

333

arg_desc->AddDefaultKey(

334 "seq-entry-acc-list"

335 "seq_entry_accession_list"

336 "accession_list, containing multiple seq entry accessions"

340

arg_desc->AddDefaultKey(

343 "file, containing seq entry in ASN.1 format"

347 string

prog_description =

"BioSample Checker\n"

;

348

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

349

prog_description,

false

);

352

SetupArgDescriptions(arg_desc.release());

363 string

bioSampleAcc = args[

"biosample-acc"

].AsString();

364 string

bioSampleFile = args[

"biosample-file"

].AsString();

365 string

bioSourceFile = args[

"biosource"

].AsString();

366 string

seqEntryAcc = args[

"seq-entry-acc"

].AsString();

367 string

seqEntryAccList = args[

"seq-entry-acc-list"

].AsString();

368 string

seqEntryFile = args[

"seq-entry-file"

].AsString();

370 if

(seqEntryAcc.empty() && seqEntryAccList.empty() && seqEntryFile.empty()) {

371 if

(bioSampleAcc.empty() && bioSampleFile.empty()) {

372

cerr <<

"Bad arguments: Need to uniquely specify biosample."

<< endl;

375 if

(!bioSampleAcc.empty() && !bioSampleFile.empty()) {

376

cerr <<

"Bad arguments: Need to uniquely specify biosample."

<< endl;

379 if

(bioSourceFile.empty()) {

380

cerr <<

"Bad arguments: Need to supply biosource."

<< endl;

385 if

(!seqEntryFile.empty() && !seqEntryAcc.empty()) {

386 auto

otherStuff = bioSampleAcc + bioSampleFile + bioSourceFile;

387 if

(!otherStuff.empty()) {

388

cerr <<

"Bad arguments: seq-entry-acc or seq-entry-file cannot go with anything else." 394 if

(!seqEntryAcc.empty()) {

395 return

xCompareSeqEntryAccession(seqEntryAcc);

398 if

(!seqEntryAccList.empty()) {

399 return

xCompareSeqEntryAccessionList(seqEntryAccList);

402 if

(!seqEntryFile.empty()) {

403 return

xCompareSeqEntryFile(seqEntryFile);

407 if

(!bioSampleAcc.empty()) {

410 if

(!bioSampleFile.empty()) {

413

cerr <<

"Internal error: utility completed without doing anything."

<< endl;

421 const string

& accession)

425

mpScope->ResetDataAndHistory();

443 const string

& filename)

449 while

(!ifstr.eof()) {

450

std::getline(ifstr, accession);

451 if

(!accession.empty()) {

453

cout <<

"Differ: Processing accession \""

<< accession <<

"\" (" 454

<< counter <<

") ---"

<< endl << endl;

455 if

(!xCompareSeqEntryAccession(accession)) {

466 const string

& seqEntryFile)

472 bool

bDeleteOnClose =

false

;

473

pInputStream =

new CNcbiIfstream

(seqEntryFile.c_str(), ios::binary);

474

bDeleteOnClose =

true

;

478

cerr <<

"Differ: Unable to open input seq-entry file"

"\n"

;

481

unique_ptr<CObjectIStream> pIs(pI);

487

cerr <<

"Differ: Unable to load input seq-entry from file"

"\n"

;

490 return

xCompareSeqEntry(pSeqEntry);

496 const string

& accession)

501

pSeqEntry = xLoadSeqEntry(accession);

504

cerr <<

"Loader: Unable to retrieve seq_entry \""

<< accession

508 return

xCompareSeqEntry(pSeqEntry);

519

cerr <<

"Differ: Unable to load input seq-entry from file."

"\n"

;

522 auto

pBioSource = xGetBioSource(pSeqEntry);

524

cerr <<

"Differ: Given sequence does not have a biosource."

<< endl;

527 auto

bioSampleAccessions = xGetBioSampleAccs(pSeqEntry);

528 if

(bioSampleAccessions.empty()) {

529

cerr <<

"Differ: Given sequence does not contain biosample links." 535 for

(

auto

bioSampleAcc: bioSampleAccessions) {

537

bioSampleAcc, *pBioSource, fusedSource, diffs)) {

553 auto

descriptors = pSeqEntry->

GetDescr

().

Get

();

554 for

(

auto

descriptor: descriptors) {

555 if

(descriptor->IsSource()) {

557

pBioSource->

Assign

(descriptor->GetSource());

572

vector<string> bioSampleAccs;

573 auto

descriptors = pSeqEntry->

GetDescr

().

Get

();

574 for

(

auto

descriptor: descriptors) {

575 if

(!descriptor->IsUser() ||

576

descriptor->GetUser().GetType().GetStr() !=

"DBLink"

) {

579 auto

descriptorData = descriptor->GetUser().GetData();

580 for

(

auto

entry: descriptorData) {

581 if

(!entry->CanGetLabel() || entry->GetLabel().GetStr() !=

"BioSample"

) {

584 if

(!entry->CanGetData()) {

587 auto

data

= entry->GetData();

588 if

(

data

.IsStr()) {

589

bioSampleAccs.push_back(

data

.GetStr());

592 if

(

data

.IsStrs()) {

593

bioSampleAccs.insert(

594

bioSampleAccs.end(),

data

.GetStrs().begin(),

data

.GetStrs().end());

599 return

bioSampleAccs;

604 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

vector< CRef< CBiosampleFieldDiff > > TBiosampleFieldDiffList

CRef< CSeq_descr > GetBiosampleData(const string &accession, bool use_dev_server=false, TBioSamples *cache=NULL)

void GenerateDiffListFromBioSource(const CSeq_descr &bioSample, const CBioSource &bioSource, TBiosampleFieldDiffList &diffs)

void PrettyPrint(const TBiosampleFieldDiffList &diffList, CNcbiOstream &ostr, size_t keyWidth=20, size_t valueWidth=40)

void PrintDiffList(const string &source, const TBiosampleFieldDiffList &diffList, CNcbiOstream &ostr)

CRef< CSeq_descr > LoadBioSampleFromAcc(const string &bioSampleAcc)

const char * BSDIFF_APP_VER

CRef< CSeq_descr > LoadBioSampleFromFile(const string &fileName)

void GenerateDiffListFromDescriptors(const CSeq_descr &bioSample, const CSeq_descr &pDescriptorSet, TBiosampleFieldDiffList &diffs)

CRef< CSeq_descr > LoadBioSource(const string &inFile)

int CompareBioSampleAccessionToDescriptors(const string &bioSampleAcc, CRef< CSeq_descr > pDescriptorSet)

int main(int argc, const char *argv[])

int CompareBioSampleAccessionToBioSource(const string &bioSampleAcc, const CBioSource &bioSource)

int CompareBioSampleFileToDescriptors(const string &bioSampleFile, CRef< CSeq_descr > pDescriptorSet)

CRef< CSeq_entry > xLoadSeqEntry(const string &)

virtual int Run(void)

Run the application.

int xCompareSeqEntryFile(const string &)

int xCompareSeqEntry(const CRef< CSeq_entry > &)

CRef< CObjectManager > mpObjmgr

int xCompareSeqEntryAccessionList(const string &)

CRef< CBioSource > xGetBioSource(CRef< CSeq_entry >)

int xCompareSeqEntryAccession(const string &)

vector< string > xGetBioSampleAccs(CRef< CSeq_entry >)

virtual void Init(void)

Initialize the application.

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

@Seq_descr.hpp User-defined methods of the data storage class.

const CSeq_descr & GetDescr(void) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

@ eString

An arbitrary string.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

ESerialDataFormat

Data file format.

@ 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.

void Read(const CObjectInfo &object)

Read object of know type.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

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.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

void Run(void)

Enter the main loop.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const Tdata & Get(void) const

Get the member data.

Lightweight interface for getting lines of data with minimal memory copying.

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

const CharType(& source)[N]

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

C++ I/O stream wrappers to compress/decompress data on-the-fly.

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