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

(

);

(

);

(

);

delta_level,

<

T,

Consumer>

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetConstraint(

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetDependency(

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

molinfo_options->

(it->first);

arg_desc->SetConstraint(

, molinfo_options);

arg_desc->AddOptionalKey(

,

,

,

);

);

biosource_options->

(it->first);

arg_desc->SetConstraint(

, biosource_options);

arg_desc->AddDefaultKey(

,

,

,

inst_mol_options->

(it->first);

arg_desc->SetConstraint(

, inst_mol_options);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetDependency(

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetConstraint(

,

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetDependency(

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetDependency(

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetCurrentGroup(

);

(entry.

()) {

}

(entry.

()) {

objects::CBioseq& bioseq = entry.

();

updated =

;

(

& orig_desc: descs) {

(new_desc->

() != orig_desc->Which() )

;

( orig_desc->Which() ) {

orig_desc->Assign(*new_desc);

descs.push_back(new_desc);

(

()[

]) {

objects::CGPipeMessageListener messageListener;

( !reader.

() ) {

ostr_seqids <<

;

);

(

()[

]) {

((*id_it)->IsLocal()) {

((*id_it)->GetLocal().IsStr()) {

(*id_it)->SetLocal().SetStr()

.insert(0,

()[

].AsString());

(*id_it)->GetLocal().GetId());

(*id_it)->SetLocal().SetStr(

()[

].AsString() + str_id);

molinfo_found=

;

source_found=

;

( desc->Which() ) {

molinfo_found=

;

( ! desc->GetMolinfo().IsSetCompleteness()

( ! desc->GetMolinfo().IsSetBiomol()

desc->SetSource().SetGenome(

);

! desc->GetSource().IsSetOrg() || ! desc->GetSource().GetOrg().IsSetOrgname()

desc->SetSource().SetOrg().Assign(*org_data.

);

(!source_found && org_data.

) {

(

()[

]) {

((*desc)->IsTitle()) {

uniprot_source_comment->

(

descs.push_back(uniprot_source_comment);

ostr_seqids << idh << endl;

(

% 100000 == 0) {

CPrimeCacheApplication::x_Process_SRA(

& istr,

( ; iter; ++iter) {

entry->SetSeq().SetInst().SetMol(

);

entry->SetSeq().SetDescr().Set().push_back(

);

(

.begin()->second.biosource) {

entry->SetSeq().SetDescr().Set().push_back(

.begin()->second.biosource);

entry->SetSeq().SetDescr().Set().push_back(*desc);

ostr_seqids <<

;

);

ostr_seqids << idh << endl;

(

% 100000 == 0) {

ostr_seqids <<

<< acc << endl;

( args[

] ) {

( !is->EndOfData() ) {

);

is->ResetLocalHooks();

( !is->EndOfData() ) {

);

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

( trimmed_bioseqs.

() || !trimmed_bioseqs.count(idh) ) {

ostr_seqids << idh <<

;

(

% 100000 == 0) {

(line.empty() || line[0] ==

) {

delta_level,

+ idh.

());

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

( trimmed_bioseqs.

() || !trimmed_bioseqs.count(idh) ) {

(delta_level == 0) {

ostr_seqids << idh <<

;

(

% 100000 == 0) {

( seq_entry.

() ) {

list<CRef<CSeq_entry> >& coll = bset.

();

( seq_entry.

() ) {

timestamp_(

(

::eCurrent).GetTimeT()),

(!parent_->m_StripInstMol.empty()) {

(

== parent_->x_StripSeqEntry(scope, *entry, trimmed_bioseqs)) {

blob.

(*entry);

parent_->m_MainChunk.OpenForWrite(parent_->m_CachePath);

= parent_->m_MainChunk.GetOffset();

parent_->m_MainChunk.Write(blob);

= parent_->m_MainChunk.GetOffset() -

;

chunk_id = parent_->m_MainChunk.GetChunkSerialNum();

parent_->x_ExtractAndIndex(*entry, timestamp_, chunk_id,

,

);

(

bioseq_it(seh); bioseq_it; ++bioseq_it) {

(*ostr_seqids_) << idh <<

;

(count_ % 100000 == 0) {

(

<<

<< count_ <<

);

ifmt = args[

].AsString();

((args[

] || args[

] || args[

] ||

args[

] || args[

] || args[

])

&& ifmt !=

&& ifmt !=

)

);

((args[

] || args[

])

&& ifmt !=

)

);

(args[

] && ifmt !=

&& ifmt !=

)

);

(args[

] || args[

] || args[

]) {

(args[

]) {

(args[

]) {

taxids_source.

(args[

].AsInputFile());

}

(args[

]) {

taxids_source.

(args[

].AsString());

col = args[

].AsInteger() - 1;

(; taxids_source; ++taxids_source) {

(line.empty() || line[0] ==

) {

vector<string> tokens;

taxid = seq_taxid.second;

(

.count(taxid)) {

+

[taxid].biosource->SetSource().SetOrg().Assign(*ref);

[taxid].orgref->Assign(*ref);

(args[

] || args[

]) {

col = args[

].AsInteger() - 1;

(args[

]) {

uniprot_sources_source.

(args[

].AsInputFile());

}

(args[

]) {

uniprot_sources_source.

(args[

].AsString());

(; uniprot_sources_source; ++uniprot_sources_source) {

(line.empty() || line[0] ==

) {

vector<string> tokens;

. AsString()] = tokens[col];

= sm_InstMolTypes.find(args[

].AsString().c_str())->second;

(args[

]) {

(!

.begin()->second.biosource) {

.begin()->second.biosource->SetSource().SetGenome(

sm_GenomeTypes.find(args[

].AsString().c_str())->second);

= sm_GenomeTypes.find(args[

].AsString().c_str())->second;

(args[

]) {

sm_BiomolTypes.find(args[

].AsString().c_str())->second);

(args[

]) {

& istr_manifest = args[

].AsInputFile();

unique_ptr<CObjectIStream> is

( !is->EndOfData() ) {

( !submit_block ) {

*is >> *submit_block;

(desc->

()) {

(!org_data.

) {

resuming_from_clean_wrapup =

;

(args[

]) {

output_file(args[

].AsString());

(!output_file.

()) {

+ output_file.

() +

);

(!line.empty() && line[0] !=

) {

previous_execution_runs.

(line.substr(15));

((resuming_from_clean_wrapup = (line ==

))) {

ostr <<

;

ostr <<

<< run <<

;

.

()->GetGeneral().GetTag().IsStr())

=

.GetSeqId()->GetGeneral().GetTag().GetStr();

ostr <<

<<

;

ostr <<

;

ostr <<

<< args[

].AsString() <<

<< endl;

= args[

].AsString() ==

(args[

]) {

list<string> mol_types;

(args[

].AsString(),

(

), mol_types, 0);

vector<string> unknown_mols;

(list<string>::const_iterator mol = mol_types.cbegin(); mol != mol_types.cend(); ++mol) {

( record != sm_InstMolTypes.end() ) {

unknown_mols.push_back(

);

(!unknown_mols.empty()) {

oss <<

;

(vector<string>::const_iterator

= unknown_mols.cbegin();

!= unknown_mols.end(); ++

) {

oss <<

;

(args[

]) {

(args[

]) {

& istr = args[

].AsInputFile();

(line.empty() || line[0] ==

) {

(ifmt ==

) {

(ifmt ==

) {

(ifmt ==

) {

x_Process_SRA(is, ostr);

(ifmt ==

) {

(ifmt ==

) {

);

(ifmt ==

) {

(ifmt ==

) {

(ifmt ==

) {

x_Process_SRA(istr, ostr);

(ifmt ==

) {

(ifmt ==

) {

);

(!ids.

()) {

(CBioseq::TInst::TExt::TDelta::Tdata, iter,

( ; id_iter; ++id_iter) {

(

argc,

* argv[])

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

size_t IndexABioseq(const objects::CBioseq &bioseq, CAsnIndex &index, CAsnIndex::TTimestamp timestamp, CAsnIndex::TChunkId chunk_id, CAsnIndex::TOffset offset, CAsnIndex::TSize size)

This is a simple BDB structure holding information about a given accession and its indexed location.

const CSeq_id * GetFirstId() const

void Pack(const CSeq_entry &entry)

void OpenForWrite(const std::string &root_path="")

void Write(const CCache_blob &cache_blob)

unsigned int GetChunkSerialNum() const

Base class for reading FASTA sequences.

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

class CInputStreamSource encapsulates details of how we supply applications with input data through s...

void InitManifest(const string &manifest)

Initialize from a manifest file.

void InitStream(CNcbiIstream &istr, const string &fname=kEmptyStr)

Initialize from a stream No ownership is claimed by this class - lifetime management of the stream is...

static void AddArguments(CArgDescriptions &arg_desc)

CConstRef< objects::COrg_ref > GetOrgRef(TTaxid taxid)

CObjectEnum(const CObjectEnum &)

CObjectEnum & operator=(const CObjectEnum &)

void SkipObject(CObjectIStream &istr, const CObjectTypeInfo &info)

CObjectEnum(Consumer consumer)

CNcbiOstream * ostr_seqids_

CRef< CObjectManager > om_

CPrimeCacheApplication * parent_

CCacheBioseq(CPrimeCacheApplication *p, CNcbiOstream *ostr)

void operator()(CBioseq &bseq)

void x_ExtractDelta(CBioseq_Handle bsh, set< CSeq_id_Handle > &delta_ids)

bool x_StripSeqEntry(CScope &scope, CSeq_entry &entry, set< CSeq_id_Handle > &trimmed_bioseqs)

void x_UpsertDescriptor(list< CRef< CSeqdesc > > &descs, CRef< CSeqdesc > new_desc)

void x_Process_Ids(const set< CSeq_id_Handle > &ids, CNcbiOstream &ostr_seqids, unsigned delta_level, size_t count)

void x_Read_Ids(CNcbiIstream &istr, set< CSeq_id_Handle > &ids)

map< string, TTaxId > m_SequenceTaxids

void x_CacheSeqEntry(CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt, set< CSeq_id_Handle > &delta_ids, size_t &count)

virtual void Init(void)

Initialize the application.

void x_Process_SeqEntry(CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt, set< CSeq_id_Handle > &delta_ids, size_t &count)

sequence::EGetIdType m_id_type

void x_ExtractAndIndex(const CSeq_entry &entry, CAsnIndex::TTimestamp timestamp, CAsnIndex::TChunkId chunk_id, CAsnIndex::TOffset offset, CAsnIndex::TSize size)

CSeq_inst::EMol m_InstMol

void x_SplitAndCacheSeqEntry(CNcbiIstream &istr, CNcbiOstream &ostr_seqids, ESerialDataFormat serial_fmt)

map< TTaxId, SOrgData > m_Orgs

CBioSource::EGenome m_Genome

set< CSeq_id_Handle > m_CachedIds

CSeqIdChunkFile m_SeqIdChunk

list< CRef< CSeqdesc > > m_other_descs

map< string, string > m_SequenceUniprotSources

CRef< CSeqdesc > m_MolInfo

set< string > m_PreviousExecutionRuns

set< CSeq_inst::EMol > m_StripInstMol

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

void x_Process_Fasta(CNcbiIstream &istr, CNcbiOstream &ostr_seqids)

set< CSeq_id_Handle > m_PreviousExecutionIds

void OpenForWrite(const std::string &root_path="")

void Write(const objects::CBioseq::TId &seq_ids)

const CSeq_descr & GetDescr(void) const

bool IsSetDescr(void) const

Skip hook for a standalone object.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

Template class for iteration on objects of class C (non-medifiable version)

iterator_bool insert(const value_type &val)

Operators to edit gaps in sequences.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#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.

SStrictId_Tax::TId TTaxId

Taxon id type.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

#define TAX_ID_FROM(T, value)

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ fAppend

Open file in append mode.

void SetCacheSize(unsigned int cache_size)

Set Berkeley DB memory cache size for the file (default is 256K).

void Open(const string &filename, EOpenMode open_mode, bool support_dirty_read=false, unsigned rec_len=0)

Open file with specified access mode.

@ eReadWriteCreate

read-write, create if it doesn't exist

void PrintRequestStop(void)

Print request stop message (for request-driven applications)

CDiagContext & GetDiagContext(void)

Get diag context instance.

void PrintRequestStart(const string &message)

Print request start message (for request-driven applications)

static CRequestContext & GetRequestContext(void)

Shortcut to CDiagContextThreadData::GetThreadData().GetRequestContext()

void SetRequestStatus(int status)

const CStopWatch & GetRequestTimer(void) const

Request execution timer.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

bool CreatePath(TCreateFlags flags=fCreate_Default) const

Create the directory path recursively possibly more than one at a time.

virtual bool Exists(void) const

Check if directory "dirname" exists.

const string & GetPath(void) const

Get entry path.

virtual bool Exists(void) const

Check existence of file.

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.

@ eSerial_AsnBinary

ASN.1 binary.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

long TFlags

binary OR of EFlags

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

void SetMaxIDLength(Uint4 max_len)

If this is set, an exception will be thrown if a Sequence ID exceeds the given length.

@ fRequireID

Reject deflines that lack IDs.

@ fAddMods

Parse defline mods and add to SeqEntry.

@ fNoUserObjs

Don't save raw deflines in User-objects.

@ fForceType

Force specified type regardless of accession.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

@ fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

void SetLocalSkipHook(CObjectIStream &stream, CSkipObjectHook *hook) const

Set local (for the specified stream) skip hook.

void ReadObject(const CObjectInfo &object)

Read child object.

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

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

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

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.

const TInst & GetInst(void) const

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

time_t GetTimeT(void) const

Get time in time_t format.

void Start(void)

Start the timer.

@ eCurrent

Use current time. See also CCurrentTime.

static bool IsSignaled(TSignalMask signals=eSignal_Any)

Check that any of specified signals is received.

static void TrapSignals(TSignalMask signals)

Sets interrupt signal handling.

@ eSignal_TERM

Termination.

void SetTimestamp(TTimestamp value)

Assign a value to Timestamp data member.

const TOrg & GetOrg(void) const

Get the Org member data.

EGenome

biological context

@ e_General

for other databases

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

void ResetAnnot(void)

Reset Annot data member.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void ResetDescr(void)

Reset Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

bool IsSetCompleteness(void) const

Check if a value has been assigned to Completeness data member.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void ResetDescr(void)

Reset Descr data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TSource & GetSource(void) const

Get the variant data.

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

void ResetAnnot(void)

Reset Annot data member.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

TComment & SetComment(void)

Select the variant.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TExt & GetExt(void) const

Get the Ext member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

EMol

molecule class in living organism

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDelta & GetDelta(void) const

Get the variant data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

bool CanGetInst(void) const

Check if it is safe to call GetInst method.

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_snoRNA

small nucleolar RNA

@ eBiomol_genomic_mRNA

reported a mix of genomic and cdna sequence

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ eBiomol_other_genetic

other genetic material

@ e_Embl

EMBL specific information.

@ e_Update_date

date of last update

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Prf

PRF specific information.

@ e_Sp

SWISSPROT specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

Setup interrupt signal handling.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

SStaticPair< const char *, const CSeq_inst::EMol > TInstMolTypeKey

CStaticPairArrayMap< const char *, const CBioSource::EGenome, PCase > TGenomeTypeMap

CStaticPairArrayMap< const char *, const CSeq_inst::EMol, PCase > TInstMolTypeMap

SStaticPair< const char *, const CBioSource::EGenome > TGenomeTypeKey

DEFINE_STATIC_ARRAY_MAP(TBiomolTypeMap, sm_BiomolTypes, db_biomol_type_name_to_enum)

static const TBiomolTypeKey db_biomol_type_name_to_enum[]

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

CStaticPairArrayMap< const char *, const CMolInfo::EBiomol, PCase > TBiomolTypeMap

static const TInstMolTypeKey db_inst_mol_type_name_to_enum[]

SStaticPair< const char *, const CMolInfo::EBiomol > TBiomolTypeKey

static const TGenomeTypeKey db_genome_type_name_to_enum[]

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Defines CRequestContext class for NCBI C++ diagnostic API.

CRef< objects::CObjectManager > om

CRef< CSeqdesc > biosource

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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