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NCBI C++ ToolKit: src/objtools/huge_asn/huge_file_process.cpp Source File

<

TLoader>

: m_loader{

.GetLoader() } {}

CBioseq_set::GetTypeInfo(),

CBioseq::GetTypeInfo(),

CSeq_entry::GetTypeInfo(),

CSeq_submit::GetTypeInfo(),

pNewEntry->Assign(*pTopEntry);

pNewEntry->SetSet().SetSeq_set().push_back(entry);

( entry && seqid.

());

processed =

(*

);

CAutoRevoker autorevoker(

);

(

:

().GetTopIds())

(

std::exception&)

(temp.IsSet() && temp.GetSet().IsSetClass() &&

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &loader_name, CHugeAsnReader *reader, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_Default)

void Open(CHugeFile *file, ILineErrorListener *pMessageListener) override

bool GetNextBlob() override

auto & GetTopEntry() const

static bool IsHugeSet(CBioseq_set::TClass setClass)

CConstRef< CSubmit_block > GetSubmitBlock() const override

CRef< CSeq_entry > GetNextSeqEntry() override

virtual void FlattenGenbankSet()

CRef< CBioseq > LoadBioseq(CConstRef< CSeq_id > seqid) const

bool ForEachEntry(CRef< CScope > scope, THandlerEntries handler)

bool ForEachBlob(THandlerBlobs)

CRef< CHugeFile > m_pHugeFile

void Open(const string &file_name, const set< TTypeInfo > *types=&g_supported_types)

static CSeq_entry_Handle GetTopLevelEntry(CBioseq_Handle beh)

bool Read(THandler handler, CRef< CSeq_id > seqid)

CHugeAsnReader & GetReader()

virtual ~CHugeFileProcess(void)

destructor

std::function< void(CConstRef< CSubmit_block >, CRef< CSeq_entry >)> THandler

static const set< TTypeInfo > g_supported_types

CRef< CHugeAsnReader > m_pReader

void OpenFile(const string &file_name)

std::function< bool(CSeq_entry_Handle &seh)> THandlerEntries

CHugeFileProcess()

constructors

std::function< bool(CHugeFileProcess &)> THandlerBlobs

static bool IsSupported(TTypeInfo info)

std::function< bool(CHugeAsnReader *, const std::list< CConstRef< CSeq_id > > &)> THandlerIds

void Open(const std::string &filename, const set< TTypeInfo > *supported_types)

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

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

static const struct type types[]

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void RemoveDataLoader(const string &loader_name, EActionIfLocked action=eThrowIfLocked)

Revoke data loader from the scope.

bool RevokeDataLoader(CDataLoader &loader)

Revoke previously registered data loader.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsTopLevelEntry(void) const

Check if this handle is top-level entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TSeq & SetSeq(void)

Select the variant.

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