// --------------------------------------------------------------------------
CSeq_entry_Handle CAsn2FastaApp::ObtainSeqEntryFromSeqEntry(
CObjectIStream& is)
// --------------------------------------------------------------------------
{
try {
CRef<CSeq_entry> se(new CSeq_entry);
is >> *se;
if (se->Which() == CSeq_entry::e_not_set) {
NCBI_THROW(CException, eUnknown,
"provided Seq-entry is empty");
}
return m_Scope->AddTopLevelSeqEntry(*se);
}
catch (CException& e) {
if (! (is.GetFailFlags() & is.eEOF)) {
ERR_POST(Error << e);
}
}
return CSeq_entry_Handle();
}
const CBioseq_Handle& CAlnVec::GetBioseqHandle(TNumrow row) const
{
TBioseqHandleCache::iterator i = m_BioseqHandlesCache.find(row);
if (i != m_BioseqHandlesCache.end()) {
return i->second;
} else {
CBioseq_Handle bioseq_handle =
GetScope().GetBioseqHandle(GetSeqId(row));
if (bioseq_handle) {
return m_BioseqHandlesCache[row] = bioseq_handle;
} else {
string errstr = string("CAlnVec::GetBioseqHandle(): ")
+ "Seq-id cannot be resolved: "
+ GetSeqId(row).AsFastaString();
NCBI_THROW(CAlnException, eInvalidSeqId, errstr);
}
}
}
bool CGeneInfoFileReader::x_GiToGeneId(int gi, list<int>& listGeneIds)
{
STwoIntRecord* pRecs;
int nRecs;
bool retval = false;
if (s_GetMemFilePtrAndLength(m_memGi2GeneFile.get(),
pRecs, nRecs))
{
retval = s_SearchSortedArray(pRecs, nRecs,
gi, 1, listGeneIds, false);
}
else
{
NCBI_THROW(CGeneInfoException, eFileNotFoundError,
"Cannot access the memory-mapped file for "
"Gi to Gene ID conversion.");
}
return retval;
}
bool CJsonOverUTTPReader::x_AddNewNode(CJsonNode::TInstance new_node)
{
if (!m_CurrentNode) {
m_CurrentNode = new_node;
return false;
} else if (m_HashValueIsExpected) {
m_HashValueIsExpected = false;
m_CurrentNode.SetByKey(m_HashKey, new_node);
} else
// The current node is either a JSON object or an array,
// because if it was a non-container node then this method
// wouldn't have been called.
if (m_CurrentNode.IsArray())
m_CurrentNode.Append(new_node);
else {
NCBI_THROW(CJsonOverUTTPException, eObjectKeyMustBeString,
"JSON-over-UTTP: Invalid object key type");
}
return true;
}
CObjectOStream* CObjectOStream::Open(ESerialDataFormat format,
CNcbiOstream& outStream,
bool bdeleteStream)
{
EOwnership deleteStream = bdeleteStream ? eTakeOwnership : eNoOwnership;
switch ( format ) {
case eSerial_AsnText:
return OpenObjectOStreamAsn(outStream, deleteStream);
case eSerial_AsnBinary:
return OpenObjectOStreamAsnBinary(outStream, deleteStream);
case eSerial_Xml:
return OpenObjectOStreamXml(outStream, deleteStream);
case eSerial_Json:
return OpenObjectOStreamJson(outStream, deleteStream);
default:
break;
}
NCBI_THROW(CSerialException,eNotImplemented,
"CObjectOStream::Open: unsupported format");
}
CAsnCache_DataLoader::SCacheInfo& CAsnCache_DataLoader::x_GetIndex()
{
if (m_IndexMap.empty()) {
NCBI_THROW(CException, eUnknown,
"setup failure: no cache objects available");
}
CFastMutexGuard LOCK(m_Mutex);
// hash to a pool of cache objects based on thread ID
int id = CThread::GetSelf();
id %= m_IndexMap.size();
TIndexMap::iterator iter = m_IndexMap.begin() + id;
if ( !iter->get() ) {
iter->reset(new SCacheInfo);
(*iter)->cache.Reset(new CAsnCache(m_DbPath));
}
return **iter;
}
CNetScheduleAPI CNetScheduleClientFactory::CreateInstance()
{
CConfig conf(m_Registry);
const CConfig::TParamTree* param_tree = conf.GetTree();
const TPluginManagerParamTree* netschedule_tree =
param_tree->FindSubNode(kNetScheduleAPIDriverName);
if (netschedule_tree) {
SNetScheduleAPIImpl* ret = m_PM_NetSchedule.CreateInstance(
kNetScheduleAPIDriverName,
TPMNetSchedule::GetDefaultDrvVers(),
netschedule_tree);
if (ret != NULL)
return ret;
}
NCBI_THROW(CNSClientFactoryException, eNSClientIsNotCreated,
"Couldn't create NetSchedule client. Check registry.");
}
void CJsonOverUTTPWriter::SendOutputBuffer()
{
const char* output_buffer;
size_t output_buffer_size;
size_t bytes_written;
do {
m_UTTPWriter.GetOutputBuffer(&output_buffer, &output_buffer_size);
for (;;) {
if (m_Pipe.Write(output_buffer, output_buffer_size,
&bytes_written) != eIO_Success) {
NCBI_THROW(CIOException, eWrite,
"Error while writing to the pipe");
}
if (bytes_written == output_buffer_size)
break;
output_buffer += bytes_written;
output_buffer_size -= bytes_written;
}
} while (m_UTTPWriter.NextOutputBuffer());
}
TMemberIndex
CChoicePointerTypeInfo::GetPtrIndex(const CChoiceTypeInfo* choiceType,
TConstObjectPtr choicePtr)
{
const CChoicePointerTypeInfo* choicePtrType =
CTypeConverter<CChoicePointerTypeInfo>::SafeCast(choiceType);
const CPointerTypeInfo* ptrType = choicePtrType->m_PointerTypeInfo;
TConstObjectPtr classPtr = ptrType->GetObjectPointer(choicePtr);
if ( !classPtr )
return choicePtrType->m_NullPointerIndex;
const CClassTypeInfo* classType =
CTypeConverter<CClassTypeInfo>::SafeCast(ptrType->GetPointedType());
const TVariantsByType& variants = choicePtrType->m_VariantsByType;
TVariantsByType::const_iterator v =
variants.find(classType->GetCPlusPlusTypeInfo(classPtr));
if ( v == variants.end() )
NCBI_THROW(CSerialException,eInvalidData,
"incompatible CChoicePointerTypeInfo type");
return v->second;
}
bool CGeneInfoFileReader::x_GeneIdToGi(int geneId, int iGiField,
list<int>& listGis)
{
SMultiIntRecord<4>* pRecs;
int nRecs;
bool retval = false;
if (s_GetMemFilePtrAndLength(m_memGene2GiFile.get(),
pRecs, nRecs))
{
retval = s_SearchSortedArray(pRecs, nRecs,
geneId, iGiField, listGis, true);
}
else
{
NCBI_THROW(CGeneInfoException, eFileNotFoundError,
"Cannot access the memory-mapped file for "
"Gene ID to Gi conversion.");
}
return retval;
}
void CBlastHitMatrixCGIApplication::x_GetSeqAnnot(CCgiContext& ctx)
{
const CNcbiRegistry & reg = ctx.GetConfig();
string blastURL = reg.Get("NetParams", "BlastURL");
string url = (string)blastURL + "?CMD=Get&RID=" + m_RID + "&FORMAT_TYPE=ASN.1&FORMAT_OBJECT=Alignment";
SConnNetInfo* net_info = ConnNetInfo_Create(NULL);
// create HTTP connection
CConn_HttpStream inHttp(url,net_info);
try {
m_Annot.Reset(new CSeq_annot);
auto_ptr<CObjectIStream> is
(CObjectIStream::Open(eSerial_AsnText, inHttp));
*is >> *m_Annot;
}
catch (CException& e) {
m_Annot.Reset();
NCBI_THROW(CBlastHitMatrixCGIException, eInvalidSeqAnnot, "Exception reading SeqAnnot via url " + url + ", exception message: " + e.GetMsg());
}
}
int CSeqDB::GetAmbigSeqAlloc(int oid,
char ** buffer,
int nucl_code,
ESeqDBAllocType strategy,
TSequenceRanges *masks) const
{
m_Impl->Verify();
if ((strategy != eMalloc) && (strategy != eNew))
{
NCBI_THROW(CSeqDBException,
eArgErr,
"Invalid allocation strategy specified.");
}
int rv = m_Impl->GetAmbigSeq(oid, buffer, nucl_code, 0, strategy, masks);
m_Impl->Verify();
return rv;
}
CSeqDB::CSeqDB(const string & dbname,
ESeqType seqtype,
CSeqDBNegativeList * nlist)
{
if (dbname.size() == 0)
{
NCBI_THROW(CSeqDBException,
eArgErr,
"Database name is required.");
}
m_Impl = s_SeqDBInit(dbname,
s_GetSeqTypeChar(seqtype),
0,
0,
true,
NULL,
nlist);
m_Impl->Verify();
}
pair<TMemberIndex, const CItemsInfo::TItemsByTag*>
CItemsInfo::GetItemsByTagInfo(void) const
{
typedef pair<TMemberIndex, const TItemsByTag*> TReturn;
TReturn ret(m_ZeroTagIndex, m_ItemsByTag.get());
if ( ret.first == kInvalidMember && ret.second == 0 ) {
CFastMutexGuard GUARD(s_ItemsMapMutex);
ret = TReturn(m_ZeroTagIndex, m_ItemsByTag.get());
if ( ret.first == kInvalidMember && ret.second == 0 ) {
{
CIterator i(*this);
if ( i.Valid() ) {
ret.first = *i-GetItemInfo(i)->GetId().GetTag();
for ( ++i; i.Valid(); ++i ) {
if ( ret.first != *i-GetItemInfo(i)->GetId().GetTag() ) {
ret.first = kInvalidMember;
break;
}
}
}
}
if ( ret.first != kInvalidMember ) {
m_ZeroTagIndex = ret.first;
}
else {
auto_ptr<TItemsByTag> items(new TItemsByTag);
for ( CIterator i(*this); i.Valid(); ++i ) {
const CItemInfo* itemInfo = GetItemInfo(i);
TTag tag = itemInfo->GetId().GetTag();
if ( !items->insert(TItemsByTag::value_type(tag, *i)).second ) {
NCBI_THROW(CSerialException,eInvalidData, "duplicate member tag");
}
}
ret.second = items.get();
m_ItemsByTag = items;
}
}
}
return ret;
}
char* CDelta_ext_PackTarget::NewSegment(CSeqUtil::TCoding coding,
TSeqPos length)
{
CRef<CDelta_seq> ds(new CDelta_seq);
CSeq_literal& lit = ds->SetLiteral();
lit.SetLength(length);
m_Obj.Set().push_back(ds);
switch (coding) {
case CSeqUtil::e_not_set:
return NULL;
#define CODING_CASE_EX(key, type, setter, len) \
case CSeqUtil::key: \
{ \
type& dest = lit.SetSeq_data().setter(); \
dest.Set().resize(len); \
return &dest.Set()[0]; \
}
#define CODING_CASE(name, type) \
CODING_CASE_EX(e_##name, type, Set##name, length)
CODING_CASE_EX(e_Ncbi2na, CNCBI2na, SetNcbi2na, (length + 3) / 4)
CODING_CASE_EX(e_Ncbi4na, CNCBI4na, SetNcbi4na, (length + 1) / 2)
// case CSeqUtil::e_Ncbi4na_expand:
// CODING_CASE(Ncbi8na, CNCBI8na)
CODING_CASE(Iupacaa, CIUPACaa)
CODING_CASE(Ncbi8aa, CNCBI8aa)
CODING_CASE(Ncbieaa, CNCBIeaa)
CODING_CASE(Ncbistdaa, CNCBIstdaa)
#undef CODING_CASE
#undef CODING_CASE_EX
default:
NCBI_THROW(CSeqUtilException, eInvalidCoding,
"CDelta_ext_PackTarget: unexpected coding");
}
}
CSeqDB::CSeqDB(const string & dbname,
ESeqType seqtype,
CSeqDBGiList * gi_list)
{
if (dbname.size() == 0)
{
NCBI_THROW(CSeqDBException,
eArgErr,
"Database name is required.");
}
char seq_type = s_GetSeqTypeChar(seqtype);
m_Impl = s_SeqDBInit(dbname,
seq_type,
0,
0,
true,
gi_list);
m_Impl->Verify();
}
int CBlastHitMatrixCGIApplication::ProcessRequest(CCgiContext &ctx)
{
// retrieve our CGI rendering params
x_GetCGIContextParams(ctx);
x_InitAppData(ctx);
bool success = true;
if(m_BlastHitMatrix->IsFileOut()) {
success = m_BlastHitMatrix->WriteToFile();
}
else {
string encoding("image/png");
CCgiResponse& response = ctx.GetResponse();
response.SetContentType(encoding);
response.WriteHeader();
success = m_BlastHitMatrix->Display(response.out());
}
if(!success) {
NCBI_THROW(CBlastHitMatrixCGIException, eImageRenderError, "Exception occured, exception message: " + m_BlastHitMatrix->GetErrorMessage());
}
return 0;
}
CRef<CGC_Assembly> CGenomicCollectionsService::GetAssembly(const string& acc_, const string& mode)
{
string acc = NStr::TruncateSpaces(acc_);
ValidateAsmAccession(acc);
CGCClient_GetAssemblyBlobRequest req;
CGCClientResponse reply;
req.SetAccession(acc);
req.SetMode(mode);
LogRequest(req);
try {
return CCachedAssembly(AskGet_assembly_blob(req, &reply)).Assembly();
} catch (CException& ex) {
if(reply.IsSrvr_error()) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}
CGeneInfoFileReader::CGeneInfoFileReader(const string& strGi2GeneFile,
const string& strGene2OffsetFile,
const string& strGi2OffsetFile,
const string& strAllGeneDataFile,
const string& strGene2GiFile,
bool bGiToOffsetLookup)
: m_strGi2GeneFile(strGi2GeneFile),
m_strGene2OffsetFile(strGene2OffsetFile),
m_strGi2OffsetFile(strGi2OffsetFile),
m_strGene2GiFile(strGene2GiFile),
m_strAllGeneDataFile(strAllGeneDataFile),
m_bGiToOffsetLookup(bGiToOffsetLookup)
{
if (!OpenBinaryInputFile(m_strAllGeneDataFile, m_inAllData))
{
NCBI_THROW(CGeneInfoException, eFileNotFoundError,
"Cannot open the Gene Data file for reading: " +
m_strAllGeneDataFile);
}
x_MapMemFiles();
}
void CSeqVector_CI::x_PrevCacheSeg()
{
_ASSERT(m_SeqMap);
TSeqPos pos = x_CachePos();
if ( pos-- == 0 ) {
// Can not go further
NCBI_THROW(CSeqVectorException, eOutOfRange,
"Can not update cache: iterator beyond start");
}
TSeqPos size = x_GetSize();
// save current cache in backup
x_SwapCache();
// update segment if needed
if ( m_Seg.IsInvalid() ) {
x_InitSeg(pos);
}
else {
while ( m_Seg && m_Seg.GetPosition() > pos ) {
x_DecSeg();
}
}
if ( !m_Seg ) {
NCBI_THROW_FMT(CSeqVectorException, eDataError,
"CSeqVector_CI: invalid sequence length: "
<<pos<<" <> "<<size);
}
// Try to re-use backup cache
if ( pos >= x_CachePos() && pos < x_CacheEndPos() ) {
m_Cache = m_CacheData.get() + pos - x_CachePos();
}
else {
// can not use backup cache
x_ResetCache();
x_UpdateCacheDown(pos);
_ASSERT(GetPos() == pos);
_ASSERT(x_CacheSize());
_ASSERT(x_CacheEndPos() == pos+1);
}
}
const CItemsInfo::TItemsByName& CItemsInfo::GetItemsByName(void) const
{
TItemsByName* items = m_ItemsByName.get();
if ( !items ) {
CFastMutexGuard GUARD(s_ItemsMapMutex);
items = m_ItemsByName.get();
if ( !items ) {
auto_ptr<TItemsByName> keep(items = new TItemsByName);
for ( CIterator i(*this); i.Valid(); ++i ) {
const CItemInfo* itemInfo = GetItemInfo(i);
const string& name = itemInfo->GetId().GetName();
if ( !items->insert(TItemsByName::value_type(name, *i)).second ) {
if ( !name.empty() )
NCBI_THROW(CSerialException,eInvalidData,
string("duplicate member name: ")+name);
}
}
m_ItemsByName = keep;
}
}
return *items;
}
CTempString CBlastDbBlob::x_ReadString(EStringFormat fmt, int * offsetp) const
{
int sz = 0;
if (fmt == eSize4) {
sz = x_ReadIntFixed<int,4>(offsetp);
} else if (fmt == eSizeVar) {
sz = x_ReadVarInt(offsetp);
}
const char * datap = "";
if (fmt == eNUL) {
CTempString ts = Str();
int zoffset = -1;
for(size_t i = *offsetp; i < ts.size(); i++) {
if (ts[i] == (char)0) {
zoffset = i;
break;
}
}
if (zoffset == -1) {
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::ReadString: Unterminated string.");
}
datap = ts.data() + *offsetp;
sz = zoffset - *offsetp;
*offsetp = zoffset+1;
} else {
datap = x_ReadRaw(sz, offsetp);
}
return CTempString(datap, sz);
}
BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::
// constructor
CSeq_data::CSeq_data(const string& value, E_Choice index)
{
// Does value have to be validated
// create seq type data holder
switch (index) {
case e_Iupacna:
case e_Iupacaa:
case e_Ncbieaa:
DoConstruct (value, index);
break;
case e_Ncbi2na:
case e_Ncbi4na:
case e_Ncbi8na:
case e_Ncbipna:
case e_Ncbi8aa:
case e_Ncbipaa:
case e_Ncbistdaa:
{
vector< char > v;
v.resize (value.size());
memcpy(&v[0], value.c_str(), value.size());
DoConstruct (v, index);
break;
}
default:
// throw error
NCBI_THROW (CException, eUnknown,
"CSeq_data constructor: Invalid E_Choice index");
}
}
string
CBlastDbFormatter::Write(const SSeqDBInitInfo& db_init_info)
{
CBlastDbMetadata dbmeta(db_init_info);
vector<string> data2write;
data2write.reserve(m_ReplacementTypes.size());
ITERATE(vector<char>, fmt, m_ReplacementTypes) {
switch (*fmt) {
case 'f': // file name
data2write.push_back(dbmeta.GetFileName());
break;
case 't': // title
data2write.push_back(dbmeta.GetTitle());
break;
case 'n': // number of sequences
data2write.push_back(dbmeta.GetNumberOfSequences());
break;
case 'l': // DB length
data2write.push_back(dbmeta.GetDbLength());
break;
case 'p': // molecule type
data2write.push_back(dbmeta.GetMoleculeType());
break;
case 'd': // date of last update
data2write.push_back(dbmeta.GetDate());
break;
case 'U': // Disk usage
data2write.push_back(dbmeta.GetDiskUsage());
break;
default:
CNcbiOstrstream os;
os << "Unrecognized format specification: '%" << *fmt << "'";
NCBI_THROW(CInvalidDataException, eInvalidInput,
CNcbiOstrstreamToString(os));
}
}
return x_Replacer(data2write);
}
void CPIDGuard::Release(void)
{
if ( !m_Path.empty() ) {
// MT-Safe protect
CFastMutexGuard LOCK(s_PidGuardMutex);
// Read info
TPid pid = 0;
unsigned int ref = 0;
CNcbiIfstream in(m_Path.c_str());
if ( in.good() ) {
in >> pid >> ref;
in.close();
if ( m_NewPID != pid ) {
// We do not own this file more
return;
}
if ( ref ) {
ref--;
}
// Check reference counter
if ( ref ) {
// Write updated reference counter into the file
CNcbiOfstream out(m_Path.c_str(),
IOS_BASE::out | IOS_BASE::trunc);
if ( out.good() ) {
out << pid << endl << ref << endl;
}
if ( !out.good() ) {
NCBI_THROW(CPIDGuardException, eWrite,
"Unable to write into PID file " + m_Path +": "
+ _T_CSTRING(NcbiSys_strerror(errno)));
}
} else {
// Remove the file
CDirEntry(m_Path).Remove();
}
}
ERR_Action Tokenize(const CTempString raw_line,
vector<CTempString>& tokens)
{
if (!m_FieldNamesExtracted) {
x_ExtractNames(raw_line);
return eRR_Skip;
}
// The field names have been extracted so tokenize and check the data
// consistency.
// Note: the only action Tokenize() returns is eRR_Continue_Data
TRowReaderStream_SingleTabDelimited::Tokenize(raw_line, tokens);
if (tokens.size() != m_NumberOfFields)
NCBI_THROW(CCRowReaderStream_IANA_TSV_Exception,
eNumberOfFieldsMismatch,
"Unexpected number of fields. The first line declared "
+ NStr::NumericToString(m_NumberOfFields) +
"fields while the current line has " +
NStr::NumericToString(tokens.size()) + " fields");
return eRR_Continue_Data;
}
CSeqDB::CSeqDB(const vector<string> & dbs,
ESeqType seqtype,
CSeqDBGiList * gi_list)
{
string dbname;
SeqDB_CombineAndQuote(dbs, dbname);
if (dbname.size() == 0)
{
NCBI_THROW(CSeqDBException,
eArgErr,
"Database name is required.");
}
m_Impl = s_SeqDBInit(dbname,
s_GetSeqTypeChar(seqtype),
0,
0,
true,
gi_list);
m_Impl->Verify();
}
CSeqDB::CSeqDB(const string & dbname,
ESeqType seqtype,
int oid_begin,
int oid_end,
bool use_mmap,
CSeqDBGiList * gi_list)
{
if (dbname.size() == 0)
{
NCBI_THROW(CSeqDBException,
eArgErr,
"Database name is required.");
}
m_Impl = s_SeqDBInit(dbname,
s_GetSeqTypeChar(seqtype),
oid_begin,
oid_end,
use_mmap,
gi_list);
m_Impl->Verify();
}
const CAuth_list& CPub::GetAuthors (void) const
{
switch (Which()) {
case CPub::e_Gen :
return (GetGen().GetAuthors());
case CPub::e_Sub :
return (GetSub().GetAuthors());
case CPub::e_Article :
return (GetArticle().GetAuthors());
case CPub::e_Book :
return (GetBook().GetAuthors());
case CPub::e_Proc :
return (GetProc().GetBook().GetAuthors());
case CPub::e_Patent :
return (GetPatent().GetAuthors());
case CPub::e_Man :
return (GetMan().GetCit().GetAuthors());
default :
NCBI_THROW(CSerialException, eNotImplemented,
"CPub::GetAuthors: unsupported entry type "
+ SelectionName(Which()));
}
}
string CGenomicCollectionsService::ValidateChrType(string chrType, string chrLoc)
{
CGCClient_ValidateChrTypeLocRequest req;
CGCClientResponse reply;
req.SetType(chrType);
req.SetLocation(chrLoc);
#ifdef _DEBUG
ostringstream ostrstrm;
ostrstrm << "Making request -" << MSerial_AsnText << req;
LOG_POST(Info << ostrstrm.str());
#endif
try {
return AskGet_chrtype_valid(req, &reply);
} catch (CException& ex) {
if(reply.Which() == CGCClientResponse::e_Srvr_error) {
NCBI_THROW(CException, eUnknown, reply.GetSrvr_error().GetDescription());
}
throw;
}
}