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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/wgsmaster_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/wgsmaster.cpp Source File

have_non_zero =

;

have_non_zero =

;

name =

.GetStr();

( name ==

||

name ==

||

name ==

||

name ==

||

name ==

) {

(name ==

) {

((*it)->GetLabel().IsStr() &&

(*it)->GetLabel().GetStr() ==

) {

= ((*it)->GetData().IsStr() ?

(

) (*it)->GetData().GetStr() :

(uo_types.count(name) == 0)

( (1 << desc.

()) &

) {

(

.HasNoSeq_entry() ) {

.x_GetBaseInfo().x_AddExistingUserObjectTypes(uo_types);

( idh.

() ) {

* text_id =

->GetTextseq_Id();

is_cage_ddbj =

;

is_cage_ddbj =

;

letters_pos = (have_nz ? 3 : 0);

(digits_pos != letters_pos+4 && digits_pos != letters_pos+6)

min_digits = ((digits_pos == letters_pos+4) ? 8 : 9);

max_digits = min_digits + 2;

(digits_count < min_digits || digits_count > max_digits)

row_id = NStr::StringToNumeric<Uint8>(acc.

(digits_pos));

= NStr::StringToNumeric<int>(acc.

(digits_pos, 2));

row_id = NStr::StringToNumeric<Uint8>(acc.

(digits_pos+2));

master_id.

(*

);

master_acc = acc.

(0, digits_pos);

master_acc.resize(acc.

(),

);

master_text_id->

();

optional_mask;

existing_mask = 0;

existing_mask |= 1 << desc.

();

= force_mask | (optional_mask & ~existing_mask);

( bs_info->IsSetDescr() ) {

(&bs_info->GetDescr());

(

chunk_id :

.x_GetDescrChunkIds() ) {

(

chunk_id : ids ) {

(

.x_IsSetDescr() ) {

(

&

:

.x_GetDescr().Get() ) {

|= 1 <<

->Which();

first_entry->x_GetBaseInfo().x_AddExistingUserObjectTypes(existing_uo_types);

descr->

().push_back(ref);

split_info.AddChunk(*chunk);

chunk->m_MasterInfo->m_AddToTSE =

;

setter->AddChunksToWait(lock->

(), split_info, 0);

setter->AddChunksToWait(first_entry->x_GetBaseInfo(), split_info,

);

setter->AddChunkToWait(seq_chunk.GetChunkId(), split_info,

);

ncbi::TMaskedQueryRegions mask

void x_AddExistingUserObjectTypes(TUserObjectTypesSet &uo_types) const

void x_AddDescrChunkId(const TDescTypeMask &types, TChunkId chunk_id)

TDescTypeMask x_GetExistingDescrMask(void) const

vector< CSeq_id_Handle > TId

const TId & GetId(void) const

TDescr & x_SetDescr(void)

const TChunkIds & x_GetBioseqChunkIds() const

CConstRef< CSeq_entry_Info > GetFirstEntry(void) const

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

const CBioseq_Base_Info & x_GetBaseInfo(void) const

const TSet & GetSet(void) const

pair< TBioseqId, TBioseq_setId > TPlace

void x_AddDescInfo(TDescTypeMask type_mask, const TBioseqId &id)

void SetLoaded(CObject *obj=0)

void x_LoadDescr(const TPlace &place, const CSeq_descr &descr)

TChunkId GetChunkId(void) const

void SetLoadListener(CRef< CTSEChunkLoadListener > listener)

const CTSE_Split_Info & GetSplitInfo(void) const

bool x_NeedUpdate(ENeedUpdate flag) const

@ fNeedUpdate_descr

specific fields of this object

void SetBioseqUpdater(CRef< CBioseqUpdater > updater)

virtual void GetBioseqsIds(TSeqIds &ids) const

vector< CSeq_id_Handle > TSeqIds

CTSE_Split_Info & GetSplitInfo(void)

CTSE_Chunk_Info & GetChunk(TChunkId chunk_id)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

virtual void Update(CBioseq_Info &seq) override

CWGSBioseqUpdaterChunk(const CSeq_id_Handle &master_idh)

virtual void Update(CBioseq_Info &seq) override

CConstRef< CSeq_descr > m_Descr

CWGSBioseqUpdaterDescr(const CSeq_id_Handle &master_idh, CConstRef< CSeq_descr > descr)

bool HasMasterId(const CBioseq_Info &seq) const

const CSeq_id_Handle & GetMasterId() const

CWGSBioseqUpdater_Base(const CSeq_id_Handle &master_idh)

CSeq_id_Handle m_MasterId

CRef< CWGSMasterInfo > m_MasterInfo

CWGSMasterChunkInfo(const CSeq_id_Handle &master_idh)

static int x_GetActualExistingDescrMask(const CBioseq_Base_Info &info)

CConstRef< CBioseq_set_Info > m_BioseqSet

CTSE_Chunk_Info::TChunkId TChunkId

void AddChunksToWait(const CBioseq_Base_Info &info, CTSE_Split_Info &split_info, int mask)

set< TChunkId > m_ChunksToWait

CRef< CWGSMasterInfo > m_MasterInfo

CWGSMasterDescrSetter(CRef< CWGSMasterChunkInfo > master_chunk_info, const CBioseq_set_Info &bset, CTSE_Split_Info &split_info, int mask)

virtual void Loaded(CTSE_Chunk_Info &chunk) override

void RegisterCallbacks(CTSE_Split_Info &split_info)

void AddChunkToWait(TChunkId chunk_id, CTSE_Split_Info &split_info, int mask)

CSeq_id_Handle m_MasterId

CWGSMasterInfo(const CSeq_id_Handle &master_idh)

CConstRef< CSeq_descr > m_OriginalMasterDescr

static void LoadWGSMaster(CDataLoader *loader, CRef< CTSE_Chunk_Info > chunk)

static void AddWGSMaster(CTSE_LoadLock &lock)

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CSeq_id::E_Choice Which(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

TTSE_LockSet GetRecordsNoBlobState(const CSeq_id_Handle &idh, EChoice choice)

The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateExceptio...

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

uint64_t Uint8

8-byte (64-bit) unsigned integer

#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.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert int to string.

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

Check if a string starts with a specified prefix value.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type find_first_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character in the matching string within the current string,...

size_type size(void) const

Return the length of the represented array.

const TData & GetData(void) const

Get the Data member data.

const TType & GetType(void) const

Get the Type member data.

vector< CRef< CUser_field > > TData

bool IsSetAccession(void) const

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

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

virtual void Reset(void)

Reset the whole object.

void SetVersion(TVersion value)

Assign a value to Version data member.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

list< CRef< CSeqdesc > > Tdata

const TUser & GetUser(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

Tdata & Set(void)

Assign a value to data member.

@ e_Embl

EMBL specific information.

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Genbank

GenBank specific info.

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Source

source of materials, includes Org-ref

const string version

version string

static const int kTSE_Place_id

bool s_HasMasterId(const CBioseq_Info &seq, const CSeq_id_Handle &master_idh)

int GetOptionalDescrMask(EDescrType type)

CConstRef< CSeq_descr > GetWGSMasterDescr(CDataLoader *loader, const CSeq_id_Handle &master_idh)

static const int kRefSeqOptionalDescrMask

static bool s_GoodLetters(CTempString s)

CSeq_id_Handle GetWGSMasterSeq_id(const CSeq_id_Handle &idh)

static const char kMasterDescrMark[]

EDescrType GetDescrType(const CSeq_id_Handle &master_seq_idh)

static const int kForceDescrMask

void AddMasterDescr(CBioseq_Info &seq, const CSeq_descr &src, EDescrType type)

bool HasWGSMasterMark(const CTSE_Info &info)

int GetForceDescrMask(EDescrType type)

static bool s_IsGoodDescr(const CSeqdesc &desc, int mask, const TUserObjectTypesSet &uo_types)

static const int kOptionalDescrMask

static const bool kAddMasterDescrToTSE

static bool s_GoodDigits(CTempString s)

static const int kGoodDescrMask

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