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

(it->first->CompareOrdered(*seqid) == 0)

(it->first->Compare(*seqid) != CSeq_id::E_SIC::e_YES)

(it->first->CompareOrdered(*seqid) == 0)

(it->first->Compare(*seqid) != CSeq_id::E_SIC::e_YES)

(descr.

()) {

(

pDesc : descr.

()) {

(pDesc && (pDesc->Which() == choice)) {

(

.m_descr) {

parentSet =

.m_parent_set;

(parentSet->m_descr) {

parentSet = parentSet->m_parent_set;

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

(it->first->Compare(*seqid) != CSeq_id::E_SIC::e_YES)

bioseq_id_mi = bioseq_info.

(

);

bioseqset_seqset_mi = bioseq_set_info.

(

);

bioseqset_annot_mi = bioseq_set_info.

(

);

seqinst_len_mi = seqinst_info.

(

);

seqinst_mol_mi = seqinst_info.

(

);

seqinst_repr_mi = seqinst_info.

(

);

bioseq_descr_mi = bioseq_info.

(

);

.ReadObject(&

.bioseq_stack.back().m_ids, (*member).GetTypeInfo());

.ReadObject(&descr, (*member).GetTypeInfo());

.bioseq_stack.back().m_descr = descr;

.ReadObject(&

.bioseq_stack.back().m_length, (*member).GetTypeInfo());

.ReadObject(&

.bioseq_stack.back().m_mol, (*member).GetTypeInfo());

.ReadObject(&

.bioseq_stack.back().m_repr, (*member).GetTypeInfo());

(*member).GetTypeInfo()->DefaultSkipData(

);

& set_rec =

.bioseq_set_stack.back();

set_rec->m_annot_pos = pos;

(*member).GetTypeInfo()->DefaultSkipData(

);

.bioseq_stack.push_back({});

parent =

.bioseq_set_stack.back();

.GetTypeInfo()->DefaultSkipData(

);

& bioseqinfo =

.bioseq_stack.back();

.push_back({pos, parent, bioseqinfo.m_length, bioseqinfo.m_descr, bioseqinfo.m_ids, bioseqinfo.m_mol, bioseqinfo.m_repr});

.bioseq_stack.pop_back();

parent =

.bioseq_set_stack.back();

.GetTypeInfo()->DefaultReadData(

, pBioseqSet);

(pBioseqSet->IsSetLevel()) {

->m_Level = pBioseqSet->GetLevel();

->m_class = pBioseqSet->GetClass();

(pBioseqSet->IsSetDescr()) {

->m_descr.Reset(&(pBioseqSet->GetDescr()));

.bioseq_set_stack.pop_back();

.GetTypeInfo()->DefaultReadData(

, pFeatId);

(pFeatId->IsLocal() && pFeatId->GetLocal().IsId())

* pObject =

.GetObjectPtr();

.GetTypeInfo()->DefaultReadData(

, pObject);

(pFeatId->IsLocal() && pFeatId->GetLocal().IsId())

obj_stream->SkipFileHeader(object_type);

obj_stream->EndOfData();

(object_type ==

|| !object_type->IsCObject())

obj_info = obj_stream->Read(object_type);

obj_stream->EndOfData();

existingPos = existingInfo.

;

newPos = newInfo.

;

(!filename.empty()) {

existingFilePos = filename +

+ existingFilePos;

newFilePos = filename +

+ newFilePos;

+ existingFilePos;

(newPos != existingPos) {

+=

+ newFilePos;

std::list<CRef<CSeq_annot>> pAnnots;

{pDescriptors, pAnnots};

bioseqset_annot_mi = bioseq_set_info.

(

);

pDescriptors->

(*top->m_descr);

(top->HasAnnot()) {

bioseqset_annot_mi.GetMemberInfo()->GetTypeInfo()->ReadData(*obj_stream, &pAnnots);

pDescriptors->

(*it->m_descr);

(

pDesc : it->m_descr->Get()) {

pDescriptors->

().push_back(pDesc);

(it->HasAnnot()) {

list< CRef< CSeq_annot > > annots;

bioseqset_annot_mi.GetMemberInfo()->GetTypeInfo()->ReadData(*obj_stream, &annots);

(!annots.empty()) {

pAnnots.splice(pAnnots.end(), std::move(annots));

{pDescriptors, pAnnots};

& parent = rec.m_parent_set;

& parent = rec.m_parent_set;

(

_class = parent->m_class;

(_class))

grandParent = parent->m_parent_set;

(!

(grandParent->m_class)) {

parent = grandParent;

grandParent = grandParent->m_parent_set;

(

: rec.m_ids) {

std::list<CRef<CSeq_annot>> pAnnots;

pTopEntry->SetSet().SetLevel() = top->m_Level.value();

pTopEntry->SetSet().SetClass() = top->m_class;

pTopEntry->SetSet().SetDescr().Assign(*pDescriptors);

(!pAnnots.empty()) {

& dest = pTopEntry->SetAnnot();

dest.splice(dest.end(), std::move(pAnnots));

std::list<CRef<CSeq_annot>> pAnnots;

(pDescriptors || !pAnnots.empty() || top->m_Level) {

top_entry->SetSet().SetLevel() = top->m_Level.value();

top_entry->SetSet().SetClass() = top->m_class;

top_entry->SetSet().SetDescr(*pDescriptors);

(!pAnnots.empty()) {

& dest = top_entry->SetAnnot();

dest.splice(dest.end(), std::move(pAnnots));

!

.empty();

addTopEntry =

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

bool IsMultiSequence() const override

bool GetNextBlob() override

const TBioseqSetInfo * FindTopObject(CConstRef< CSeq_id > seqid) const

CConstRef< CSeqdesc > GetClosestDescriptor(const TBioseqInfo &info, CSeqdesc::E_Choice choice) const

unique_ptr< CObjectIStream > MakeObjStream(TFileSize pos) const

auto & GetBiosets() const

CRef< CSerialObject > ReadAny()

void x_ThrowDuplicateId(const TBioseqSetInfo &existingInfo, const TBioseqSetInfo &newInfo, const CSeq_id &duplicateId)

virtual void x_SetBioseqSetHooks(CObjectIStream &objStream, TContext &context)

std::list< CConstRef< CSeq_id > > m_top_ids

TBioseqIndex m_bioseq_index

static bool IsHugeSet(CBioseq_set::TClass setClass)

std::tuple< CRef< CSeq_descr >, std::list< CRef< CSeq_annot > > > x_GetTopLevelDescriptors() const

const CBioseq_set::TClass * m_pTopLevelClass

ILineErrorListener * mp_MessageListener

bool HasNestedGenbankSets() const

bool IsNotJustLocalOrGeneral() const

CConstRef< CSubmit_block > GetSubmitBlock() const override

CRef< CSeq_entry > GetNextSeqEntry() override

virtual CRef< CSeq_entry > LoadSeqEntry(const TBioseqSetInfo &info, eAddTopEntry add_top_entry=eAddTopEntry::yes) const

TSeqIdTypes m_seq_id_types

void ExtendReadHooks(t_more_hooks hooks)

CConstRef< CSubmit_block > m_submit_block

TStreamPos GetCurrentPos() const

TBioseqSetList::const_iterator m_Current

const TBioseqInfo * FindBioseq(CConstRef< CSeq_id > seqid) const

const CBioseq_set::TClass * GetTopLevelClass() const

bool HasLoneProteins() const

TBioseqSetList m_FlattenedSets

TBioseqList m_bioseq_list

TBioseqSetList m_bioseq_set_list

virtual void FlattenGenbankSet()

virtual void x_SetHooks(CObjectIStream &objStream, TContext &context)

virtual void x_SetFeatIdHooks(CObjectIStream &objStream)

TBioseqSetIndex m_FlattenedIndex

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

virtual void x_SetBioseqHooks(CObjectIStream &objStream, TContext &context)

std::list< t_more_hooks > m_more_hooks

std::function< void(CObjectIStream &)> t_more_hooks

CRef< CSeq_entry > m_top_entry

unique_ptr< CObjectIStream > MakeObjStream(std::streampos pos=0) const

TTypeInfo RecognizeContent(std::streampos pos)

std::streampos m_filesize

@Seq_descr.hpp User-defined methods of the data storage class.

Base class for all serializable objects.

constexpr bool test(T _Pos) const

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

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

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

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

static const TObjectType * SafeCast(TTypeInfo type)

string GetLabel(const CSeq_id &id)

CMemberIterator FindMember(const string &memberName) const

Find class member by its name.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#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.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_General

for other databases

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_genbank

converted genbank

const Tdata & Get(void) const

Get the member data.

E_Choice

Choice variants.

bool IsSet(void) const

Check if a value has been assigned to data member.

Tdata & Set(void)

Assign a value to data member.

static CConstRef< CSeqdesc > s_GetDescriptor(const CSeq_descr &descr, CSeqdesc::E_Choice choice)

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

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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

void SetLocalSkipHook(const CObjectTypeInfo &obj_type_info, CObjectIStream &istr, _Func _func)

void SetLocalReadHook(const CObjectTypeInfo &obj_type_info, CObjectIStream &ostr, _Func _func)

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

static CS_CONTEXT * context

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