C++ GroupInfo类代码示例

void
QuotaObject::UpdateSize(int64_t aSize)
{
  QuotaManager* quotaManager = QuotaManager::Get();
  NS_ASSERTION(quotaManager, "Shouldn't be null!");

  MutexAutoLock lock(quotaManager->mQuotaMutex);

  if (!mOriginInfo) {
    return;
  }

  GroupInfo* groupInfo = mOriginInfo->mGroupInfo;

  if (groupInfo->IsForTemporaryStorage()) {
    quotaManager->mTemporaryStorageUsage -= mSize;
  }
  groupInfo->mUsage -= mSize;
  mOriginInfo->mUsage -= mSize;

  mSize = aSize;

  mOriginInfo->mUsage += mSize;
  groupInfo->mUsage += mSize;
  if (groupInfo->IsForTemporaryStorage()) {
    quotaManager->mTemporaryStorageUsage += mSize;
  }
}

void NsAdapterCatalog::updateGroup(const GroupInfo& group) throw (DmException)
{
  // gid may not be initialized
  GroupInfo g = this->getGroup(group.name);
  wrapCall(dpns_modifygrpmap(g.getUnsigned("gid"),
                             (char*)group.name.c_str(),
                             group.getLong("banned")));
}

std::vector<GroupInfo> BuiltInAuthn::getGroups(void) throw (DmException)
{
  std::vector<GroupInfo> groups;
  GroupInfo group;
  struct group* ent;
  
  while ((ent = getgrent()) != NULL) {
    group.clear();
    group.name   = ent->gr_name;
    group["gid"] = ent->gr_gid;
  }
  
  return groups;
}

int plNetMsgGroupOwner::IPeekBuffer(hsStream* stream, uint32_t peekOptions)
{
    int bytes=plNetMsgServerToClient::IPeekBuffer(stream, peekOptions);
    if (bytes)
    {
        int i, num;
        stream->LogReadLE(&num,"GroupOwnerNum");
        fGroups.resize(num);
        for(i=0;i<num;i++)
        {
            GroupInfo gr;
            gr.Read(stream);
            fGroups[i]=gr;
        }
        
        bytes=stream->GetPosition();
    }
    
    return bytes;
}

void AuthnOracle::updateGroup(const GroupInfo& group) throw (DmException)
{
  occi::Statement* stmt = getPreparedStatement(this->conn_, STMT_UPDATE_GROUP);
  
  try {
    stmt->setInt(1, group.getLong("banned"));
    stmt->setString(2, group.name);
    stmt->executeUpdate();
    this->conn_->commit();
    this->conn_->terminateStatement(stmt);
  }
  catch (occi::SQLException& ex) {
    this->conn_->rollback();
    throw DmException(DM_INTERNAL_ERROR, ex.getMessage());
  }
}

bool suPHP::GroupInfo::operator==(const GroupInfo& ginfo) const {
    if (this->getGid() == ginfo.getGid())
        return true;
    else
        return false;
}

//.........这里部分代码省略.........

	for (int i = 6; i < argc; i++) {
		if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
		if (!strcmp(argv[i], "-b")) {
			genBamF = true;
			inpSamType = argv[i + 1][0];
			strcpy(inpSamF, argv[i + 2]);
			if (atoi(argv[i + 3]) == 1) {
				strcpy(fn_list, argv[i + 4]);
				pt_fn_list = (char*)(&fn_list);
			}
		}
		if (!strcmp(argv[i], "-q")) { quiet = true; }
		if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; }
		if (!strcmp(argv[i], "--sampling")) { bamSampling = true; }
		if (!strcmp(argv[i], "--seed")) {
		  hasSeed = true;
		  int len = strlen(argv[i + 1]);
		  seed = 0;
		  for (int k = 0; k < len; k++) seed = seed * 10 + (argv[i + 1][k] - '0');
		}
		if (!strcmp(argv[i], "--calc-evaluation-score")) {
			calcEvalScore = true;
			nb_r = atof(argv[i + 1]);
			nb_p = atof(argv[i + 2]);
			L = atoi(argv[i + 3]);
			w = atoi(argv[i + 4]);
		}
	}

	general_assert(nThreads > 0, "Number of threads should be bigger than 0!");

	verbose = !quiet;

	//basic info loading
	sprintf(refF, "%s.seq", refName);
	refs.loadRefs(refF);
	M = refs.getM();

	sprintf(tiF, "%s.ti", refName);
	transcripts.readFrom(tiF);

	sprintf(cntF, "%s.cnt", statName);
	fin.open(cntF);

	general_assert(fin.is_open(), "Cannot open " + cstrtos(cntF) + "! It may not exist.");

	fin>>N0>>N1>>N2>>N_tot;
	fin.close();

	general_assert(N1 > 0, "There are no alignable reads!");

	if ((READ_INT_TYPE)nThreads > N1) nThreads = N1;

	//set model parameters
	mparams.M = M;
	mparams.N[0] = N0; mparams.N[1] = N1; mparams.N[2] = N2;
	mparams.refs = &refs;

	sprintf(mparamsF, "%s.mparams", imdName);
	fin.open(mparamsF);

	general_assert(fin.is_open(), "Cannot open " + cstrtos(mparamsF) + "It may not exist.");

	fin>> mparams.minL>> mparams.maxL>> mparams.probF;
	int val; // 0 or 1 , for estRSPD
	fin>>val;
	mparams.estRSPD = (val != 0);
	fin>> mparams.B>> mparams.mate_minL>> mparams.mate_maxL>> mparams.mean>> mparams.sd;
	fin>> mparams.seedLen;
	fin.close();

	//run EM
	switch(read_type) {
	case 0 : EM<SingleRead, SingleHit, SingleModel>(); break;
	case 1 : EM<SingleReadQ, SingleHit, SingleQModel>(); break;
	case 2 : EM<PairedEndRead, PairedEndHit, PairedEndModel>(); break;
	case 3 : EM<PairedEndReadQ, PairedEndHit, PairedEndQModel>(); break;
	default : fprintf(stderr, "Unknown Read Type!\n"); exit(-1);
	}

	if (calcEvalScore) {
		CalcEvalScore ces(refs, nb_r, nb_p, L, w, statName);
		sprintf(scoreF, "%s.score", outName);
		ces.writeScoresTo(scoreF);
		
		char groupF[STRLEN];
		GroupInfo gi;
		sprintf(groupF, "%s.grp", argv[1]);
		gi.load(groupF);

		ces.generateExpressionFiles(gi, transcripts, scoreF);
	}

	time_t b = time(NULL);

	printTimeUsed(a, b, "EM.cpp");

	return 0;
}

void* calcCI_batch(void* arg) {
	float *itsamples, *gtsamples;
	ifstream fin;
	CIParams *ciParams = (CIParams*)arg;

	itsamples = new float[nSamples];
	gtsamples = new float[nSamples];

	fin.open(tmpF, ios::binary);
	streampos pos = streampos(gi.spAt(ciParams->start_gene_id)) * nSamples * FLOATSIZE;
	fin.seekg(pos, ios::beg);

	int cnt = 0;
	for (int i = ciParams->start_gene_id; i < ciParams->end_gene_id; i++) {
		int b = gi.spAt(i), e = gi.spAt(i + 1);
		memset(gtsamples, 0, FLOATSIZE * nSamples);
		for (int j = b; j < e; j++) {
			for (int k = 0; k < nSamples; k++) {
				fin.read((char*)(&itsamples[k]), FLOATSIZE);
				gtsamples[k] += itsamples[k];
			}
			calcCI(nSamples, itsamples, iso_tau[j].lb, iso_tau[j].ub);
		}
		calcCI(nSamples, gtsamples, gene_tau[i].lb, gene_tau[i].ub);

		++cnt;
		if (verbose && cnt % 1000 == 0) { printf("In thread %d, %d genes are processed for CI calculation!\n", ciParams->no, cnt); }
	}

	fin.close();

	delete[] itsamples;
	delete[] gtsamples;

	return NULL;
}

int main(int argc, char* argv[]) {
	ifstream fin;
	bool quiet = false;

	if (argc < 5) {
		printf("Usage : rsem-run-em refName read_type sampleName sampleToken [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n");
		printf("  refName: reference name\n");
		printf("  read_type: 0 single read without quality score; 1 single read with quality score; 2 paired-end read without quality score; 3 paired-end read with quality score.\n");
		printf("  sampleName: sample's name, including the path\n");
		printf("  sampleToken: sampleName excludes the path\n");
		printf("  -p: number of threads which user wants to use. (default: 1)\n");
		printf("  -b: produce bam format output file. (default: off)\n");
		printf("  -q: set it quiet\n");
		printf("  --gibbs-out: generate output file used by Gibbs sampler. (default: off)\n");
		printf("  --sampling: sample each read from its posterior distribution when bam file is generated. (default: off)\n");
		printf("// model parameters should be in imdName.mparams.\n");
		exit(-1);
	}

	time_t a = time(NULL);

	strcpy(refName, argv[1]);
	read_type = atoi(argv[2]);
	strcpy(outName, argv[3]);
	sprintf(imdName, "%s.temp/%s", argv[3], argv[4]);
	sprintf(statName, "%s.stat/%s", argv[3], argv[4]);

	nThreads = 1;

	genBamF = false;
	bamSampling = false;
	genGibbsOut = false;
	pt_fn_list = pt_chr_list = NULL;

	for (int i = 5; i < argc; i++) {
		if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
		if (!strcmp(argv[i], "-b")) {
			genBamF = true;
			inpSamType = argv[i + 1][0];
			strcpy(inpSamF, argv[i + 2]);
			if (atoi(argv[i + 3]) == 1) {
				strcpy(fn_list, argv[i + 4]);
				pt_fn_list = (char*)(&fn_list);
			}
		}
		if (!strcmp(argv[i], "-q")) { quiet = true; }
		if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; }
		if (!strcmp(argv[i], "--sampling")) { bamSampling = true; }
	}

	general_assert(nThreads > 0, "Number of threads should be bigger than 0!");

	verbose = !quiet;

	//basic info loading
	sprintf(refF, "%s.seq", refName);
	refs.loadRefs(refF);
	M = refs.getM();
	sprintf(groupF, "%s.grp", refName);
	gi.load(groupF);
	m = gi.getm();

	sprintf(tiF, "%s.ti", refName);
	transcripts.readFrom(tiF);

	sprintf(cntF, "%s.cnt", statName);
	fin.open(cntF);

	general_assert(fin.is_open(), "Cannot open " + cstrtos(cntF) + "! It may not exist.");

	fin>>N0>>N1>>N2>>N_tot;
	fin.close();

	general_assert(N1 > 0, "There are no alignable reads!");

	if ((READ_INT_TYPE)nThreads > N1) nThreads = N1;

	//set model parameters
	mparams.M = M;
	mparams.N[0] = N0; mparams.N[1] = N1; mparams.N[2] = N2;
	mparams.refs = &refs;

	sprintf(mparamsF, "%s.mparams", imdName);
	fin.open(mparamsF);

	general_assert(fin.is_open(), "Cannot open " + cstrtos(mparamsF) + "It may not exist.");

	fin>> mparams.minL>> mparams.maxL>> mparams.probF;
	int val; // 0 or 1 , for estRSPD
	fin>>val;
	mparams.estRSPD = (val != 0);
	fin>> mparams.B>> mparams.mate_minL>> mparams.mate_maxL>> mparams.mean>> mparams.sd;
	fin>> mparams.seedLen;
	fin.close();

	//run EM
	switch(read_type) {
	case 0 : EM<SingleRead, SingleHit, SingleModel>(); break;
	case 1 : EM<SingleReadQ, SingleHit, SingleQModel>(); break;
	case 2 : EM<PairedEndRead, PairedEndHit, PairedEndModel>(); break;
//.........这里部分代码省略.........

void writeResults(ModelType& model, double* counts) {
	double denom;
	char outF[STRLEN];
	FILE *fo;

	sprintf(modelF, "%s.model", statName);
	model.write(modelF);

	//calculate tau values
	double *tau = new double[M + 1];
	memset(tau, 0, sizeof(double) * (M + 1));

	denom = 0.0;
	for (int i = 1; i <= M; i++) 
	  if (eel[i] >= EPSILON) {
	    tau[i] = theta[i] / eel[i];
	    denom += tau[i];
	  }   

	general_assert(denom > 0, "No alignable reads?!");

	for (int i = 1; i <= M; i++) {
		tau[i] /= denom;
	}

	//isoform level results
	sprintf(outF, "%s.iso_res", imdName);
	fo = fopen(outF, "w");
	for (int i = 1; i <= M; i++) {
		const Transcript& transcript = transcripts.getTranscriptAt(i);
		fprintf(fo, "%s%c", transcript.getTranscriptID().c_str(), (i < M ? '\t' : '\n'));
	}
	for (int i = 1; i <= M; i++)
		fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n'));
	for (int i = 1; i <= M; i++)
		fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
	for (int i = 1; i <= M; i++) {
		const Transcript& transcript = transcripts.getTranscriptAt(i);
		fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < M ? '\t' : '\n'));
	}
	fclose(fo);

	//gene level results
	sprintf(outF, "%s.gene_res", imdName);
	fo = fopen(outF, "w");
	for (int i = 0; i < m; i++) {
		const string& gene_id = transcripts.getTranscriptAt(gi.spAt(i)).getGeneID();
		fprintf(fo, "%s%c", gene_id.c_str(), (i < m - 1 ? '\t' : '\n'));
	}
	for (int i = 0; i < m; i++) {
		double sumC = 0.0; // sum of counts
		int b = gi.spAt(i), e = gi.spAt(i + 1);
		for (int j = b; j < e; j++) sumC += counts[j];
		fprintf(fo, "%.2f%c", sumC, (i < m - 1 ? '\t' : '\n'));
	}
	for (int i = 0; i < m; i++) {
		double sumT = 0.0; // sum of tau values
		int b = gi.spAt(i), e = gi.spAt(i + 1);
		for (int j = b; j < e; j++) sumT += tau[j];
		fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
	}
	for (int i = 0; i < m; i++) {
		int b = gi.spAt(i), e = gi.spAt(i + 1);
		for (int j = b; j < e; j++) {
			fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : (i < m - 1 ? '\t' :'\n')));
		}
	}
	fclose(fo);

	delete[] tau;

	if (verbose) { printf("Expression Results are written!\n"); }
}

int main(int argc, char* argv[]) {
	bool quiet = false;

	if (argc < 6) {
		printf("Usage : rsem-parse-alignments refName imdName statName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
		exit(-1);
	}

	strcpy(fn_list, "");
	read_type = 0;
	if (argc > 6) {
		for (int i = 6; i < argc; i++) {
			if (!strcmp(argv[i], "-t")) {
				read_type = atoi(argv[i + 1]);
			}
			if (!strcmp(argv[i], "-l")) {
				strcpy(fn_list, argv[i + 1]);
			}
			if (!strcmp(argv[i], "-tag")) {
				SamParser::setReadTypeTag(argv[i + 1]);
			}
			if (!strcmp(argv[i], "-q")) { quiet = true; }
		}
	}

	verbose = !quiet;

	sprintf(groupF, "%s.grp", argv[1]);
	gi.load(groupF);
	sprintf(tiF, "%s.ti", argv[1]);
	transcripts.readFrom(tiF);

	sprintf(datF, "%s.dat", argv[2]);
	sprintf(cntF, "%s.cnt", argv[3]);

	init(argv[2], argv[4][0], argv[5]);

	hit_out.open(datF);

	string firstLine(99, ' ');
	firstLine.append(1, '\n');		//May be dangerous!
	hit_out<<firstLine;

	switch(read_type) {
	case 0 : parseIt<SingleRead, SingleHit>(parser); break;
	case 1 : parseIt<SingleReadQ, SingleHit>(parser); break;
	case 2 : parseIt<PairedEndRead, PairedEndHit>(parser); break;
	case 3 : parseIt<PairedEndReadQ, PairedEndHit>(parser); break;
	}

	hit_out.seekp(0, ios_base::beg);
	hit_out<<N[1]<<" "<<nHits<<" "<<read_type;

	hit_out.close();

	//cntF for statistics of alignments file
	ofstream fout(cntF);
	fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
	fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
	fout<<nHits<<" "<<read_type<<endl;
	fout<<"0\t"<<N[0]<<endl;
	for (iter = counter.begin(); iter != counter.end(); iter++) {
		fout<<iter->first<<'\t'<<iter->second<<endl;
	}
	fout<<"Inf\t"<<N[2]<<endl;
	fout.close();

	release();

	if (verbose) { printf("Done!\n"); }

	return 0;
}

int main(int argc, char* argv[]) {
	if (argc < 8) {
		printf("Usage: rsem-calculate-credibility-intervals reference_name sample_name sampleToken confidence nCV nSpC nMB [-p #Threads] [-q]\n");
		exit(-1);
	}

	confidence = atof(argv[4]);
	nCV = atoi(argv[5]);
	nSpC = atoi(argv[6]);
	nMB = atoi(argv[7]);

	nThreads = 1;
	quiet = false;
	for (int i = 8; i < argc; i++) {
		if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
		if (!strcmp(argv[i], "-q")) quiet = true;
	}
	verbose = !quiet;

	sprintf(refF, "%s.seq", argv[1]);
	refs.loadRefs(refF, 1);
	M = refs.getM();
	sprintf(groupF, "%s.grp", argv[1]);
	gi.load(groupF);
	m = gi.getm();

	nSamples = nCV * nSpC;
	cvlen = M + 1;
	assert(nSamples > 0 && cvlen > 1); // for Buffter.h: (bufsize_type)nSamples

	sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
	sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
	sprintf(tmpF, "%s.tmp", imdName);
	sprintf(cvsF, "%s.countvectors", imdName);

	sprintf(modelF, "%s.model", statName);
	FILE *fi = fopen(modelF, "r");
	general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
	assert(fscanf(fi, "%d", &model_type) == 1);
	fclose(fi);

	// Phase I
	switch(model_type) {
	case 0 : sample_theta_vectors_from_count_vectors<SingleModel>(); break;
	case 1 : sample_theta_vectors_from_count_vectors<SingleQModel>(); break;
	case 2 : sample_theta_vectors_from_count_vectors<PairedEndModel>(); break;
	case 3 : sample_theta_vectors_from_count_vectors<PairedEndQModel>(); break;
	}

	// Phase II
	calculate_credibility_intervals(imdName);

	/*
	sprintf(command, "rm -f %s", tmpF);
	int status = system(command);
	if (status != 0) {
		fprintf(stderr, "Cannot delete %s!\n", tmpF);
		exit(-1);
	}
	*/

	return 0;
}

void calculate_credibility_intervals(char* imdName) {
	FILE *fo;
	char outF[STRLEN];
	int num_threads = nThreads;

	iso_tau = new CIType[M + 1];
	gene_tau = new CIType[m];

	assert(M > 0);
	int quotient = M / num_threads;
	if (quotient < 1) { num_threads = M; quotient = 1; }
	int cur_gene_id = 0;
	int num_isoforms = 0;

	// A just so so strategy for paralleling
	ciParamsArray = new CIParams[num_threads];
	for (int i = 0; i < num_threads; i++) {
		ciParamsArray[i].no = i;
		ciParamsArray[i].start_gene_id = cur_gene_id;
		num_isoforms = 0;

		while ((m - cur_gene_id > num_threads - i - 1) && (i == num_threads - 1 || num_isoforms < quotient)) {
			num_isoforms += gi.spAt(cur_gene_id + 1) - gi.spAt(cur_gene_id);
			++cur_gene_id;
		}

		ciParamsArray[i].end_gene_id = cur_gene_id;
	}

	threads = new pthread_t[num_threads];

	/* set thread attribute to be joinable */
	pthread_attr_init(&attr);
	pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);

	// paralleling
	for (int i = 0; i < num_threads; i++) {
		rc = pthread_create(&threads[i], &attr, &calcCI_batch, (void*)(&ciParamsArray[i]));
		pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
	}
	for (int i = 0; i < num_threads; i++) {
		rc = pthread_join(threads[i], &status);
		pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
	}

	// releasing resources

	/* destroy attribute */
	pthread_attr_destroy(&attr);
	delete[] threads;

	delete[] ciParamsArray;

	//isoform level results
	sprintf(outF, "%s.iso_res", imdName);
	fo = fopen(outF, "a");
	for (int i = 1; i <= M; i++)
		fprintf(fo, "%.6g%c", iso_tau[i].lb, (i < M ? '\t' : '\n'));
	for (int i = 1; i <= M; i++)
		fprintf(fo, "%.6g%c", iso_tau[i].ub, (i < M ? '\t' : '\n'));
	fclose(fo);

	//gene level results
	sprintf(outF, "%s.gene_res", imdName);
	fo = fopen(outF, "a");
	for (int i = 0; i < m; i++)
		fprintf(fo, "%.6g%c", gene_tau[i].lb, (i < m - 1 ? '\t' : '\n'));
	for (int i = 0; i < m; i++)
		fprintf(fo, "%.6g%c", gene_tau[i].ub, (i < m - 1 ? '\t' : '\n'));
	fclose(fo);

	delete[] iso_tau;
	delete[] gene_tau;

	if (verbose) { printf("All credibility intervals are calculated!\n"); }
}