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NCBI C++ ToolKit: src/objtools/flatfile/buf_data_loader.cpp Source File

* ret =

;

(

.IsGenbank() ||

.IsEmbl() ||

.IsPir() ||

.IsSwissprot() ||

.IsDdbj() ||

.IsTpg() ||

.IsTpe() ||

.IsTpd()) {

}

(

.IsGeneral()) {

(

.GetGeneral().IsSetDb() &&

.GetGeneral().GetDb() ==

&&

.GetGeneral().IsSetTag() &&

.GetGeneral().GetTag().IsId()) {

(;

< pp->

;

++) {

cur_block->

= vernum;

cur_block->

= pp;

(

(q) > 78 && q[28] ==

&& q[63] ==

&&

pp->

- 1;

(div < eptr && *div ==

)

(*eptr ==

&& eptr >

)

(*eptr ==

&& eptr >

)

eptr = ptr + entry.

.

;

bioseq->

().push_back(new_id);

entry->

.

= entry_str;

ix =

(pp, accession.c_str(), ver, *entry);

name(

);

old_indx = pp->curindx;

* ptr = entry->

.

;

* eptr = ptr + entry->

.

;

pp->entrylist[pp->curindx]->drop =

;

(pp->entrylist[ix]->bases == 0) {

pp->curindx = old_indx;

pp->entrylist[ix]->bases;

User-defined methods of the data storage class.

char * GetGenBankBlock(TDataBlkList &chain, char *ptr, Int2 *retkw, char *eptr)

unique_ptr< unsigned char[]> GetDNAConv(void)

unique_ptr< unsigned char[]> GetProteinConv(void)

char * GetEmblBlock(TDataBlkList &chain, char *ptr, short *retkw, Parser::EFormat format, char *eptr)

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

bool GetEmblInstContig(const DataBlk &entry, objects::CBioseq &bioseq, ParserPtr pp)

static bool get_accession_from_id(const CSeq_id &id, string &accession, int &version)

static CRef< CBioseq > parse_entry(ParserPtr pp, char *entry_str, const string &accession, int ver, const CSeq_id &id)

static char * get_sequence_text(ParserPtr parser, const string &accession, int version)

static int add_entry(ParserPtr pp, const char *acc, Int2 vernum, const DataBlk &entry)

static void AddToIndexBlk(const DataBlk &entry, IndexblkPtr ibp, Parser::EFormat format)

size_t CheckOutsideEntry(ParserPtr pp, const char *acc, Int2 vernum)

static CRef< CBioseq > get_bioseq(ParserPtr pp, const DataBlk &entry, const CSeq_id &id)

static DataBlk * make_entry(char *entry_str)

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, Parser *params, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)

void x_LoadData(const CSeq_id_Handle &idh, CTSE_LoadLock &lock)

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

static const string & GetLoaderNameFromArgs(Parser *)

virtual bool CanGetBlobById() const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

EntryBlk * GetEntryData() const

void SetEntryData(EntryBlk *)

struct DataBlk::@1166 mBuf

iterator_bool insert(const value_type &val)

#define ERR_FORMAT_MissingEnd

#define ParFlat_ENTRYNODE

int fta_atoi(string_view sv)

bool fta_StartsWith(const char *s1, string_view s2)

bool StringEquN(const char *s1, const char *s2, size_t n)

bool StringEqu(const char *s1, const char *s2)

void StringCpy(char *d, const char *s)

void StringNCpy(char *d, const char *s, size_t n)

size_t StringLen(const char *s)

#define FtaErrPost(sev, level,...)

bool GetGenBankInstContig(const DataBlk &entry, CBioseq &bsp, ParserPtr pp)

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

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,...

const value_type & GetValue(void) const

CBlobIdFor< CSeq_id_Handle > CBlobIdSeq_id

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CDataSource * GetDataSource(void) const

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

EIsDefault

Flag defining if the data loader is included in the "default" group.

TRegisterInfo GetRegisterInfo(void)

static void RegisterInObjectManager(CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)

Register the loader only if the name is not yet registered in the object manager.

@ eAll

all blobs (main and external)

@ eCore

?only seq-entry core?

@ eBioseq

main blob with complete bioseq

@ eBioseqCore

main blob with bioseq core (no seqdata and annots)

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

int16_t Int2

2-byte (16-bit) signed 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.

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

Convert int to string.

@ eSeq_code_type_iupacna

IUPAC 1 letter nuc acid code.

bool IsSetAccession(void) const

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

TVersion GetVersion(void) const

Get the Version member data.

bool IsSetVersion(void) const

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

const TAccession & GetAccession(void) const

Get the Accession member data.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

@ eStrand_ss

single strand

@ ParFlat_COL_MOLECULE_NEW

@ ParFlat_COL_TOPOLOGY_NEW

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const string version

version string

CRef< objects::CObjectManager > om

char *(* ff_get_entry_v_pp)(const char *accession, Int2 vernum, Parser *pp)

char *(* ff_get_entry)(const char *accession)

char *(* ff_get_entry_pp)(const char *accession, Parser *pp)

vector< IndexblkPtr > entrylist

char *(* ff_get_entry_v)(const char *accession, Int2 vernum)

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