Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asn2flat_8cpp_source.html below:

NCBI C++ ToolKit: src/app/asn2flat/asn2flat.cpp Source File

()

;

()

;

<

_TMethod,

... TArgs>

(_TMethod method, TArgs&& ... args);

<

_TMethod,

... TArgs>

(_TMethod method,

* app, CAsn2FlatApp::TThreadStatePool::TUniqPointer thread_state, TArgs ... args);

TThreadPool m_thread_pool;

unique_ptr<ncbi::grpcapi::dbsnp::primary_track::DbSnpPrimaryTrack::Stub> m_SNPTrackStub;

arg_desc->SetUsageContext(

,

);

arg_desc->SetCurrentGroup(

);

arg_desc->SetConstraint(

,

arg_desc->AddFlag(

,

);

arg_desc->SetConstraint(

,

&(*

,

,

,

,

,

));

arg_desc->SetCurrentGroup(

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetCurrentGroup(

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetDependency(

,

arg_desc->AddFlag(

,

);

,

filename = args[name].AsString();

<<

<< endl;

(args[

] || args[

] || args[

]) {

((args[

] && ! args[

]) || args[

].AsString() ==

) {

gb_loader->CGBDataLoader::SetAlwaysLoadExternal(

);

host = cfg.

(

,

,

);

port = cfg.

(

,

,

);

hostport = host +

+ port;

grpc::CreateChannel(hostport, grpc::InsecureChannelCredentials());

= ! args[

] && (args[

] || cfg.

(

,

,

));

<<

<< endl;

<<

<< endl;

<<

<< endl;

<<

<< endl;

has_o_args = has_o_arg || has_on_arg || has_og_arg || has_or_arg || has_op_arg || has_ou_arg;

view = args[

].AsString();

(args[

]) {

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

) {

.OpenFile(args[

].AsString(), args[

] ?

: &edit::CHugeFileProcess::g_supported_types);

(args[

] && args[

] && !args[

] &&

(content == CBioseq_set::GetTypeInfo()) {

= args[

] ?

+ args[

].AsString() :

;

(args[

]) {

<

_TMethod,

... TArgs>

success = method(app,

, std::forward<TArgs>(args)...);

(!success) app->

=

;

<

_TMethod,

... TArgs>

);

member = std::mem_fn(method);

calleable =

<decltype(member), std::decay_t<TArgs>...>;

m_thread_pool.OneShot(calleable, member,

, std::move(thread_state), std::forward<TArgs>(args)...);

std::thread(calleable, member,

, std::move(thread_state), std::forward<TArgs>(args)...).detach();

calleable(member,

, std::move(thread_state), std::forward<TArgs>(args)...);

(reader && seqid) {

entry = reader->LoadSeqEntry(seqid);

(

pSubmitBlock = reader->GetSubmitBlock(); pSubmitBlock) {

pSeqSubmit->SetSub().Assign(*pSubmitBlock);

pSeqSubmit->SetData().SetEntrys().push_back(entry);

propagate =

()[

];

success =

;

(

: idlist) {

asn_type = args[

].AsString();

(asn_info ==

)

(asn_type ==

) {

asn_info = CSeq_entry::GetTypeInfo();

}

(asn_type ==

) {

asn_info = CBioseq::GetTypeInfo();

}

(asn_type ==

) {

asn_info = CBioseq_set::GetTypeInfo();

}

(asn_type ==

) {

asn_info = CSeq_submit::GetTypeInfo();

(asn_info == CSeq_entry::GetTypeInfo()) {

(! is->EndOfData()) {

.m_Scope->RemoveTopLevelSeqEntry(seh);

}

(asn_info == CBioseq::GetTypeInfo()) {

(! is->EndOfData()) {

.m_Scope->RemoveTopLevelSeqEntry(seh);

}

(asn_info == CBioseq_set::GetTypeInfo()) {

(! is->EndOfData()) {

.m_Scope->RemoveTopLevelSeqEntry(seh);

}

(asn_info == CSeq_submit::GetTypeInfo()) {

(! is->EndOfData()) {

}

(asn_type ==

) {

(! is->EndOfData()) {

strNextTypeName = is->PeekNextTypeName();

.m_Scope->RemoveTopLevelSeqEntry(seh);

.m_cleanup.BasicCleanup(sub, options);

seh =

.m_Scope->GetSeq_entryHandle(*e);

seh =

.m_Scope->AddTopLevelSeqEntry(*e);

.m_Scope->RemoveTopLevelSeqEntry(seh);

HandleSeqSubmit(

, *sub);

HandleSeqEntryHandle(

, seh);

(tseh.

()) {

.m_cleanup.BasicCleanup(*tmp_se, options);

(tmp_se->

()) {

.m_Scope->AddTopLevelSeqEntry(*se);

.m_Scope->AddTopLevelSeqEntry(*entry);

.m_Scope->ResetDataAndHistory();

(args[

]) {

&

= args[

].AsString();

(

==

) {

}

(

==

) {

}

(

==

) {

bDeleteOnClose =

;

pInputStream =

(args[

].AsString(), ios::binary);

bDeleteOnClose =

;

pInputStream = &std::cin;

unique_ptr<CObjectIStream>{pI};

( args[

] ) {

= args[

] || args[

] || args[

];

= args[

];

}

(

) {

.m_FFGenerator->SetAnnotSelector().IncludeNamedAnnotAccession(

);

(args[

] || args[

].AsString() ==

) {

.m_FFGenerator->SetAnnotSelector().SetExcludeExternal(

);

(args[

] || args[

].AsString() ==

) {

.m_FFGenerator->SetAnnotSelector().SetResolveAll();

(args[

]) {

.m_FFGenerator->SetAnnotSelector().SetResolveDepth(args[

].AsInteger());

(args[

]) {

.m_FFGenerator->SetAnnotSelector().SetMaxSearchSegments(args[

].AsInteger());

(args[

]) {

.m_FFGenerator->SetAnnotSelector().SetMaxSearchTime(

(args[

].AsDouble()));

(args[

].AsInteger());

(args[

]) {

& locn = args[

].AsString();

(args[

]) {

loc.

().SetFrom(from);

loc.

().SetTo(to);

loc.

().SetStrand(strand);

(entry.

()) {

it->GetSeq();

it->GetSeq();

acc_prefix = acc.substr(0, 2);

(acc_prefix ==

|| acc_prefix ==

||

acc_prefix ==

|| acc_prefix ==

) {

snp_status = m_SNPTrackStub->ForSeqId(&

, request, &reply);

(snp_status.ok()) {

(! na_acc.empty())

(args[

] || args[

] || args[

] || args[

]) {

.m_FFGenerator->Generate(loc, seh.

(), *flatfile_os, { flatfile_os });

(

.m_FFGenerator.NotEmpty()) {

.m_FFGenerator->SetFeatTree(

);

(

.m_Scope.NotEmpty()) {

.m_Scope->ResetDataAndHistory();

(

.m_Scope.Empty()) {

.m_Scope->AddDefaults();

(m_SNPDataLoader) {

.m_Scope->AddDataLoader(m_SNPDataLoader->GetLoaderNameFromArgs());

(

.m_FFGenerator.Empty())

(args[

] && args[

] && args[

].AsString() ==

) {

*os << (unwrap ?

:

) << endl;

list<string> split_args;

vector<const char*> new_argv;

(argc==2 && argv && argv[1] && strchr(argv[1],

))

it = split_args.begin();

(it != split_args.end())

(

!= split_args.end() &&

((it->front() ==

&& it->back() !=

) ||

(it->front() ==

&& it->back() !=

)))

it->append(

); it->append(*

);

(

& rec: split_args)

(rec.front()==

&& rec.back()==

)

rec=rec.substr(1, rec.length()-2);

argc = 1 +

(split_args.size());

new_argv.reserve(argc);

new_argv.push_back(argv[0]);

(

& s : split_args)

new_argv.push_back(s.c_str());

std::cerr << s.c_str() <<

;

argv = new_argv.data();

User-defined methods of the data storage class.

static const CDataLoadersUtil::TLoaders default_loaders

#define asn2flat_app_main

void Init() override

Initialize the application.

void x_GetLocation(const CSeq_entry_Handle &entry, const CArgs &args, CSeq_loc &loc) const

static void x_OneShotMethod(_TMethod method, const CAsn2FlatApp *app, CAsn2FlatApp::TThreadStatePool::TUniqPointer thread_state, TArgs ... args)

int x_GenerateTraditionally(unique_ptr< CObjectIStream > is, TFFContext &context, const CArgs &args) const

bool HandleSeqSubmit(TFFContext &context, CObjectIStream &is) const

TResourcePool< TFFContext > TThreadStatePool

TThreadStatePool m_state_pool

void x_FFGenerate(CSeq_entry_Handle seh, TFFContext &context) const

int x_AddSNPAnnots(CBioseq_Handle &bsh, TFFContext &context) const

bool HandleSeqId(TFFContext &context, const edit::CHugeAsnReader *reader, CConstRef< CSeq_id > seqid) const

TSeqPos x_GetTo(const CArgs &args) const

unique_ptr< CObjectIStream > x_OpenIStream(const CArgs &args) const

void HandleTextId(TFFContext &context, const string &id) const

edit::CHugeFileProcess m_huge_process

CSeq_entry_Handle ObtainSeqEntryFromBioseq(TFFContext &context, CObjectIStream &is, bool report) const

void x_CreateFlatFileGenerator(TFFContext &context, const CArgs &args) const

std::atomic< bool > m_stopit

unique_ptr< ICanceled > m_pCanceledCallback

CRef< CCDDDataLoader > m_CDDDataLoader

void x_ResetContext(TFFContext &context)

TSeqPos x_GetFrom(const CArgs &args) const

CBioseq_Handle x_DeduceTarget(const CSeq_entry_Handle &entry) const

bool HandleSeqEntryHandle(TFFContext &context, CSeq_entry_Handle seh) const

std::atomic< bool > m_Exception

bool WrapINSDSet(bool unwrap)

ENa_strand x_GetStrand(const CArgs &args) const

int Run() override

Run the application.

void x_InitNewContext(TFFContext &context)

CSeq_entry_Handle ObtainSeqEntryFromBioseqSet(TFFContext &context, CObjectIStream &is, bool report) const

bool x_OneShot(_TMethod method, TArgs &&... args)

CSeq_entry_Handle ObtainSeqEntryFromSeqEntry(TFFContext &context, CObjectIStream &is, bool report) const

CFFMultiSourceFileSet m_writers

bool SetFlatfileOstream(eFlatFileCodes _code, const string &name)

CFlatFileConfig::CGenbankBlockCallback TGenbankBlockCallback

decltype(TFFContext::m_streams) fileset_type

int x_GenerateBatchMode(unique_ptr< CObjectIStream > is)

CRef< CObjectManager > m_Objmgr

bool HandleSeqEntry(TFFContext &context, CRef< CSeq_entry > se) const

CBioseq_set_EditHandle –.

static string GetLoaderNameFromArgs(void)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

@ eClean_FlatfileHTMLMode

@ eClean_FlatfileGenerator

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void AddArgumentDescriptions(CArgDescriptions &arg_desc, TLoaders loaders=fDefault)

Add a standard set of arguments used to configure the object manager.

static void AddArgumentDescriptions(CArgDescriptions &args)

void SetHTMLFormatter(CRef< IHTMLFormatter > html_fmt)

bool ShowSNPFeatures(void) const

void FromArguments(const CArgs &args)

CFlatFileConfig & SetHideSNPFeatures(bool val=true)

bool BasicCleanup(void) const

SAnnotSelector & SetAnnotSelector(void)

CGBReleaseFile is a utility class to ease the processing of Genbank release files one Seq-entry at a ...

CGRPCClientContext – client context for NCBI gRPC services.

CGetSeqLocFromStringHelper_ReadLocFromText(CScope *scope)

virtual CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags)

void SetNcbiURLBase(const string &path)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const SLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

CWrapINSDSet(CAsn2FlatApp *app)

CZipStreamDecompressor – zlib based decompression stream processor.

void SetDepth(size_t depth)

void SetUseMT(bool use_mt)

fileset_type MakeNewFileset()

void Open(enum_type _enum, const std::string &filename)

static std::unique_ptr< Stub > NewStub(const std::shared_ptr< ::grpc::ChannelInterface > &channel, const ::grpc::StubOptions &options=::grpc::StubOptions())

const std::string & na_track_acc_with_filter() const

void set_gi(::uint64_t value)

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

The NCBI C++ standard methods for dealing with std::string.

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char location[]

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const string & GetProgramDisplayName(void) const

Get the application's "display" name.

const CVersionAPI & GetFullVersion(void) const

Get the program version information.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

@ 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)

@ fCheckFileHeader

Check (and skip) gzip file header on decompression stage.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

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

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.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

@ eContent

Untagged human-readable accession or the like.

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

Override Assign() to incorporate cache invalidation.

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

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

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

TLoader * GetLoader(void) const

Get pointer to the loader.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CDataLoader * FindDataLoader(const string &loader_name) const

Try to find a registered data loader by name.

static void SetDefaultKeepExternalAnnotsForEdit(bool keep=true)

Set new application-wide KeepExternalAnnotsForEdit flag.

TClass GetClass(void) const

TSet SelectSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the empty Seq-entry to Bioseq-set.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< TObject > GetCompleteObject(void) const

TInst_Mol GetInst_Mol(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

Remove current seqset-entry from its location.

CConstRef< TObject > GetCompleteObject(void) const

TSeq SelectSeq(CBioseq &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TInst_Length GetInst_Length(void) const

bool IsSetClass(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

@ eReturn

Return default value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Truncate whitespace in a string.

@ eCurrent

Use current time. See also CCurrentTime.

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...

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static void TrapSignals(TSignalMask signals)

Sets interrupt signal handling.

@ eSignal_USR1

User defined signal 1.

const SBuildInfo & GetBuildInfo() const

Get build info (date and tag, if set)

CTime GetBuildTime(void) const

Converts 'date' parameter to CTime.

ENa_strand

strand of nucleic acid

E_Choice Which(void) const

Which variant is currently selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

TSet & SetSet(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if variant Set is selected.

TSeq & SetSeq(void)

Select the variant.

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

@ eClass_segset

segmented sequence + parts

@ e_not_set

No variant selected.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

@ eMol_na

just a nucleic acid

bool IsSetData(void) const

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

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

bool IsEntrys(void) const

Check if variant Entrys is selected.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::EXPIRES expires

const GenericPointer< typename T::ValueType > T2 value

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Setup interrupt signal handling.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

CRef< CSeq_loc > GetSeqLocFromString(const string &text, const CSeq_id *id, CGetSeqLocFromStringHelper *helper)

Utility macros and typedefs for exploring NCBI objects from seq.asn.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CFFMultiSourceFileSet::fileset_type m_streams

CRef< CFlatFileGenerator > m_FFGenerator

static CS_CONTEXT * context

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4