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

50 static const size_t delimiter_len = sizeof(delimiter) - 1; // exclude \0 53 static void s_ConvertConcatStringToVectorOfString(const string & s, vector<string> & v) 58 size_t pos_find = s.find(delimiter, pos_start); 59 if(pos_find == string::npos) 61 size_t length = pos_find - pos_start; 62 v.push_back(s.substr(pos_start, length)); 63 pos_start = pos_find + delimiter_len; 66 v.push_back(s.substr(pos_start, s.size() - pos_start )); 69 static void s_MergeAlignSet(CSeq_align_set & final_set, const CSeq_align_set & input_set) 71 CSeq_align_set::Tdata & final_list = final_set.Set(); 72 const CSeq_align_set::Tdata & input_list = input_set.Get(); 74 CSeq_align_set::Tdata::const_iterator input_it = input_list.begin(); 75 CSeq_align_set::Tdata::iterator final_it = final_list.begin(); 76 while(input_it != input_list.end()) 81 (*final_it)->GetNamedScore(CSeq_align::eScore_EValue, final_evalue); 82 (*input_it)->GetNamedScore(CSeq_align::eScore_EValue, input_evalue); 84 if(input_evalue == final_evalue) 86 //Pulling a trick here to keep the program flow simple 87 //Replace the final evalue with input bitscore and vice versa 88 (*final_it)->GetNamedScore(CSeq_align::eScore_BitScore, input_evalue); 89 (*input_it)->GetNamedScore(CSeq_align::eScore_BitScore, final_evalue); 92 if(input_evalue < final_evalue) 94 CSeq_align_set::Tdata::const_iterator start_input_it = input_it; 97 const CSeq_id & id_prev = (*input_it)->GetSeq_id(1); 99 if(input_it == input_list.end()) 104 if(! id_prev.Match((*input_it)->GetSeq_id(1))) 110 final_list.insert(final_it, start_input_it, input_it); 116 const CSeq_id & id_prev = (*final_it)->GetSeq_id(1); 119 if(final_it == final_list.end()) 124 if(! id_prev.Match((*final_it)->GetSeq_id(1))) 130 if(final_it == final_list.end()) 132 final_list.insert(final_it, input_it, input_list.end()); 139 static CRef<CSearchResultSet> s_CombineSearchSets(vector<CRef<CSearchResultSet> > & t, unsigned int num_of_threads) 141 CRef<CSearchResultSet> aggregate_search_result_set (new CSearchResultSet()); 142 aggregate_search_result_set->clear(); 144 for(unsigned int i=0; i < t[0]->GetNumQueries(); i++) 146 vector< CRef<CSearchResults> > thread_results; 147 thread_results.push_back (CRef<CSearchResults> (&((*(t[0]))[i]))); 148 const CSeq_id & id = *(thread_results[0]->GetSeqId()); 150 for(unsigned int d=1; d < num_of_threads; d++) 152 thread_results.push_back ((*(t[d]))[id]); 155 CRef<CSeq_align_set> align_set(new CSeq_align_set); 156 TQueryMessages aggregate_messages; 157 for(unsigned int d=0; d< num_of_threads; d++) 159 if(thread_results[d]->HasAlignments()) 161 CConstRef<CSeq_align_set> thread_align_set = thread_results[d]->GetSeqAlign(); 162 if(align_set->IsEmpty()) 164 align_set->Set().insert(align_set->Set().begin(), 165 thread_align_set->Get().begin(), 166 thread_align_set->Get().end()); 170 s_MergeAlignSet(*align_set, *thread_align_set); 173 aggregate_messages.Combine(thread_results[d]->GetErrors()); 176 TMaskedQueryRegions query_mask; 177 thread_results[0]->GetMaskedQueryRegions(query_mask); 178 CRef<CSearchResults> aggregate_search_results (new CSearchResults(thread_results[0]->GetSeqId(), 181 thread_results[0]->GetAncillaryData(), 183 thread_results[0]->GetRID())); 184 aggregate_search_result_set->push_back(aggregate_search_results); 188 return aggregate_search_result_set; 192 static void s_ModifyVolumePaths(vector<string> & rps_database) 194 for(unsigned int i=0; i < rps_database.size(); i++) 196 size_t found = rps_database[i].find("

.pal");

197

if(string::npos != found)

198

rps_database[i]= rps_database[i].substr(0, found);

202

static bool s_SortDbSize(const pair<string, Int8> & a, const pair<string, Int8> & b)

204

return(a.second > b.second);

207

static void s_MapDbToThread(vector<string> & db, unsigned int num_of_threads)

209

unsigned int db_size = static_cast<unsigned int>(db.size());

210

vector <pair <string, Int8> > p;

212

for(unsigned int i=0; i < db_size; i++)

215

CSeqDB::FindVolumePaths(db[i], CSeqDB::eProtein, path, NULL, true);

216

_ASSERT(path.size() == 1);

217

CFile f(path[0]+".loo");

218

Int8 length = f.GetLength();

219

_ASSERT(length > 0 );

220

//Scale down, just in case

221

p.push_back(make_pair(db[i], length/1000));

224

sort(p.begin(), p.end(),s_SortDbSize);

226

db.resize(num_of_threads);

227

vector<Int8> acc_size(num_of_threads, 0);

229

for(unsigned char i=0; i < num_of_threads; i++)

232

acc_size[i] = p[i].second;

235

for(unsigned int i= num_of_threads; i < db_size; i++)

237

unsigned int min_index = 0;

238

for(unsigned int j=1; j<num_of_threads; j++)

240

if(acc_size[j] < acc_size[min_index])

244

acc_size[min_index] += p[i].second;

245

db[min_index] = db[min_index] + delimiter + p[i].first;

250

CRef<CSearchResultSet> s_RunLocalRpsSearch(const string & db,

251

CBlastQueryVector & query_vector,

252

CRef<CBlastOptionsHandle> opt_handle)

254

CSearchDatabase search_db(db, CSearchDatabase::eBlastDbIsProtein);

255

CRef<CLocalDbAdapter> db_adapter(new CLocalDbAdapter(search_db));

256

CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(query_vector));

258

CLocalBlast lcl_blast(queries, opt_handle, db_adapter);

259

CRef<CSearchResultSet> results = lcl_blast.Run();

265

class CRPSThread : public CThread

268

CRPSThread(CRef<CBlastQueryVector> query_vector,

270

CRef<CBlastOptions> options);

275

CRef<CSearchResultSet> RunTandemSearches(void);

277

CRPSThread(const CRPSThread &);

278

CRPSThread & operator=(const CRPSThread &);

281

CRef<CBlastOptionsHandle> m_opt_handle;

282

CRef<CBlastQueryVector> m_query_vector;

287

CRPSThread::CRPSThread(CRef<CBlastQueryVector> query_vector,

289

CRef<CBlastOptions> options):

290

m_query_vector(query_vector)

293

m_opt_handle.Reset(new CBlastRPSOptionsHandle(options));

295

s_ConvertConcatStringToVectorOfString(db, m_db);

298

void* CRPSThread::Main(void)

300

CRef<CSearchResultSet> * result = new (CRef<CSearchResultSet>);

303

*result = s_RunLocalRpsSearch(m_db[0],

309

*result = RunTandemSearches();

315

CRef<CSearchResultSet> CRPSThread::RunTandemSearches(void)

317

unsigned int num_of_db = static_cast<unsigned int>(m_db.size());

318

vector<CRef<CSearchResultSet> > results;

320

for(unsigned int i=0; i < num_of_db; i++)

322

results.push_back(s_RunLocalRpsSearch(m_db[i],

327

return s_CombineSearchSets(results, num_of_db);

330

/* CThreadedRpsBlast */

331

CLocalRPSBlast::CLocalRPSBlast(CRef<CBlastQueryVector> query_vector,

333

CRef<CBlastOptionsHandle> options,

334

unsigned int num_of_threads):

335

m_num_of_threads(num_of_threads),

337

m_opt_handle(options),

338

m_query_vector(query_vector),

341

CSeqDB::FindVolumePaths(db, CSeqDB::eProtein, m_rps_databases, NULL, true, true);

342

m_num_of_dbs = static_cast<unsigned int>(m_rps_databases.size());

343

if( 1 == m_num_of_dbs)

345

m_num_of_threads = kDisableThreadedSearch;

349

void CLocalRPSBlast::x_AdjustDbSize(void)

351

if(m_opt_handle->GetOptions().GetEffectiveSearchSpace()!= 0)

354

if(m_opt_handle->GetOptions().GetDbLength()!= 0)

357

CSeqDB db(m_db_name, CSeqDB::eProtein);

359

Uint8 db_size = db.GetTotalLengthStats();

360

int num_seq = db.GetNumSeqsStats();

363

db_size = db.GetTotalLength();

366

num_seq = db.GetNumSeqs();

368

m_opt_handle->SetOptions().SetDbLength(db_size);

369

m_opt_handle->SetOptions().SetDbSeqNum(num_seq);

374

CRef<CSearchResultSet> CLocalRPSBlast::Run(void)

376

if(1 != m_num_of_dbs)

381

if(kDisableThreadedSearch == m_num_of_threads)

383

if(1 == m_num_of_dbs)

385

return s_RunLocalRpsSearch(m_db_name, *m_query_vector, m_opt_handle);

389

s_ModifyVolumePaths(m_rps_databases);

391

vector<CRef<CSearchResultSet> > results;

392

for(unsigned int i=0; i < m_num_of_dbs; i++)

394

results.push_back(s_RunLocalRpsSearch(m_rps_databases[i],

399

return s_CombineSearchSets(results, m_num_of_dbs);

405

return RunThreadedSearch();

409

CRef<CSearchResultSet> CLocalRPSBlast::RunThreadedSearch(void)

412

s_ModifyVolumePaths(m_rps_databases);

414

if((kAutoThreadedSearch == m_num_of_threads) ||

415

(m_num_of_threads > m_rps_databases.size()))

417

//Default num of thread : a thread for each db

418

m_num_of_threads = static_cast<unsigned int>(m_rps_databases.size());

420

else if(m_num_of_threads < m_rps_databases.size())

422

// Combine databases, modified the size of rps_database

423

s_MapDbToThread(m_rps_databases, m_num_of_threads);

426

vector<CRef<CSearchResultSet> * > thread_results(m_num_of_threads, NULL);

427

vector <CRPSThread* > thread(m_num_of_threads, NULL);

428

vector<CRef<CSearchResultSet> > results;

430

for(unsigned int t=0; t < m_num_of_threads; t++)

432

// CThread destructor is protected, all threads destory themselves when terminated

433

thread[t] = (new CRPSThread(m_query_vector, m_rps_databases[t], m_opt_handle->SetOptions().Clone()));

437

for(unsigned int t=0; t < m_num_of_threads; t++)

439

thread[t]->Join(reinterpret_cast<void**> (&thread_results[t]));

442

for(unsigned int t=0; t < m_num_of_threads; t++)

444

results.push_back(*(thread_results[t]));

447

CRef<CBlastRPSInfo> rpsInfo = CSetupFactory::CreateRpsStructures(m_db_name,

448

CRef<CBlastOptions> (&(m_opt_handle->SetOptions())));

449

return s_CombineSearchSets(results, m_num_of_threads);

Declares the CBlastRPSOptionsHandle class.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Main class to perform a BLAST search on the local machine.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines NCBI C++ exception handling.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Multi-threading â mutexes; rw-locks; semaphore.

Multi-threading â classes, functions, and features.

Defines: CTimeFormat - storage class for time format.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

static const char delimiter[]

Declares the CLocalRPSBlast class.

Defines BLAST database access classes.

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