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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/processors_8cpp_source.html below:

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

77 #define NCBI_USE_ERRCODE_X Objtools_Rd_Process 105  for

(

size_t i

= 0;

i

<

sizeof

(m); ++p, ++

i

) {

109

m = (m << 8) | (*p & 0xff);

115  class

COSSReader :

public IReader 118  typedef

vector<char> TOctetString;

119  typedef

list<TOctetString*> TOctetStringSequence;

121

COSSReader(

const

TOctetStringSequence&

in

)

123

m_CurVec(

in

.begin())

130  size_t

* bytes_read = 0)

132  size_t

pending = x_Pending();

135

*bytes_read =

count

;

137  if

( pending == 0 ) {

149  size_t

pending = x_Pending();

155  void

x_SetVec(

void

)

158

m_CurSize = m_CurVec == m_Input.end()? 0: (**m_CurVec).size();

160  size_t

x_Pending(

void

)

163  while

( (

size

= m_CurSize - m_CurPos) == 0 &&

164

m_CurVec != m_Input.end() ) {

171  const

TOctetStringSequence& m_Input;

172

TOctetStringSequence::const_iterator m_CurVec;

191  const char

*

data

=

static_cast<const char

*

>

(

buffer

);

214 #define GB_STATS_STOP(action, stat, size) \ 215  LogStat(action, blob_id, stat, r, size, result) 227

: m_Dispatcher(&dispatcher)

258  "CProcessor::ProcessObjStream() is not implemented"

);

267  if

( !

data

.IsSetData() ) {

269  "CProcessor::ProcessBlobFromID2Data() no data"

);

271  if

(

data

.GetData_format() !=

data

.eData_format_asn_binary ) {

273  "CProcessor::ProcessBlobFromID2Data() is not implemented"

);

278  switch

(

data

.GetData_compression() ) {

294  "CProcessor::ProcessBlobFromID2Data() is not implemented"

);

317  if

( !TPackStrings::GetDefault() ) {

321

TPackStrings::SetDefault(

false

);

365  type

.FindMember(

"key"

).SetLocalReadHook(

in

,

387  type

.FindMember(

"val"

).SetLocalReadHook(

in

,

391  type

.FindMember(

"key"

).SetLocalReadHook(

in

,

419  static

atomic<TIntId> gi_offset;

420  static

atomic<bool> initialized;

421  if

( !initialized.load(memory_order_acquire) ) {

422

gi_offset.store(

NCBI_PARAM_TYPE

(GENBANK, GI_OFFSET)::GetDefault(), memory_order_relaxed);

423

initialized.store(

true

, memory_order_release);

425  return

gi_offset.load(memory_order_relaxed);

435  TGi

gi =

id

.GetGi();

441  else if

(

id

.IsGeneral() ) {

442  CDbtag

& dbtag =

id

.SetGeneral();

448  const string

& s =

tag

.GetStr();

464  if

(

tag

.GetId8(id8) &&

467  tag

.SetId8(id8 + gi_offset);

482  TGi

gi =

id

.GetGi();

490  if

(

OffsetId

(*seq_id, gi_offset) ) {

511  switch

( req.

Which

() ) {

549  OffsetGi

(it->SetStart(), gi_offset);

559  if

( (*it2)->IsGi() ) {

560  OffsetGi

((*it2)->SetGi(), gi_offset);

565  if

( it->SetId().IsGi() ) {

566  OffsetGi

(it->SetId().SetGi(), gi_offset);

579

it->second.m_SNP_annot_Info->OffsetGi(gi_offset);

675  "double load of "

<<blob_id<<

'/'

<<chunk_id);

684  size_t

data_size = 0;

693  "CProcessor_ID1: read data"

,

703  result

.SetAndSaveBlobState(blob_id, entry.second);

712  "CProcessor_ID1: attached entry"

,

718  if

( writer &&

version

>= 0 ) {

731  switch

( reply.

Which

() ) {

742  if

(

info

.GetBlob_state() < 0 ) {

752  if

(

info

.GetSuppress() & 5 ) {

754

(

info

.GetSuppress() == 4)

758  if

(

info

.GetWithdrawn() ) {

763  if

(

info

.GetConfidential() ) {

789  "ID1server-back.error "

<<

error

);

792  "ID1server-back.error "

<<

error

);

794  "CProcessor_ID1::GetSeq_entry: " 795  "ID1server-back.error "

<<

error

);

802  "CProcessor_ID1::GetSeq_entry: " 803  "bad ID1server-back type: "

<<reply.

Which

());

812  switch

( reply.

Which

() ) {

829  _ASSERT

(writer && byte_source);

831

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

852

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

904  "CProcessor_ID1_SNP: " 905  "double load of "

<<blob_id<<

'/'

<<chunk_id);

909  size_t

data_size = 0;

919  "CProcessor_ID1: read SNP data"

,

928  result

.SetAndSaveBlobState(blob_id, entry.second);

931  if

( writer &&

version

>= 0 ) {

946

*entry.first, entry.second, *set_info);

959  "CProcessor_ID1: attached entry"

,

1005  "double load of "

<<blob_id<<

'/'

<<chunk_id);

1016  size_t

data_size = 0;

1020

obj_stream >> *seq_entry;

1025  "CProcessor_SE: read seq-entry"

,

1037  "CProcessor_SE: attached entry"

,

1043  result

.GetAddWGSMasterDescr() ) {

1065  const char

* processor_name)

const 1067  if

( !

result

.IsLoadedBlobVersion(blob_id) ) {

1068  ERR_POST_X

(4,

"CProcessor_"

<<processor_name<<

"::ProcessObjStream: " 1069  "blob version is not set"

);

1073  ERR_POST_X

(5,

"CProcessor_"

<<processor_name<<

"::ProcessObjStream: " 1074  "state no_data is set"

);

1118  "CProcessor_SE_SNP: " 1119  "double load of "

<<blob_id<<

'/'

<<chunk_id);

1123  size_t

data_size = 0;

1137  "CProcessor_SE_SNP: parse SNP data"

,

1176  "CProcessor_SE_SNP: attached SNP entry to OM"

,

1227  "CProcessor_St_SE: read state"

,

1231  result

.SetAndSaveBlobState(blob_id, blob_state);

1245

blob_state, writer);

1307

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1330

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1353

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1362

obj_stream << seq_entry;

1379

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1429  "CProcessor_St_SE_SNPT: " 1430  "double load of "

<<blob_id<<

'/'

<<chunk_id);

1434  result

.SetAndSaveBlobState(blob_id, blob_state);

1449  "CProcessor_St_SE_SNPT: read SNP table"

,

1450  double

(data_size));

1455  SaveSNPBlob

(

result

, blob_id, chunk_id, writer, *seq_entry, blob_state, *set_info);

1465  "CProcessor_St_SE_SNPT: attached SNP table"

,

1466  double

(data_size));

1482

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1536

blob_state = obj_stream.

ReadInt4

();

1537

obj_stream >>

data

;

1541  "CProcessor_ID2: read data"

,

1559  if

( chunk_id >= 0 ) {

1564  "double load of "

<<blob_id<<

'/'

<<chunk_id);

1569  "double load of "

<<blob_id<<

'/'

<<chunk_id);

1572  size_t

data_size = 0;

1573  switch

(

data

.GetData_type() ) {

1577  if

( split_version != 0 || skel ) {

1580  "plain Seq-entry with extra ID2S-Split-Info"

);

1585  "plain Seq-entry in chunk reply"

);

1596  "CProcessor_ID2: parsed Seq-entry"

,

1600  result

.SetAndSaveBlobState(blob_id, blob_state);

1610  result

.GetAddWGSMasterDescr() ) {

1616  "CProcessor_ID2: attached Seq-entry"

,

1624  if

(

data

.GetData_format() ==

data

.eData_format_asn_binary &&

1625  data

.GetData_compression() ==

data

.eData_compression_none &&

1633

blob_state, writer,

data

.GetData());

1647  "plain ID2S-Split-Info in non-main reply"

);

1658  "CProcessor_ID2: parsed split info"

,

1663  if

( !with_skeleton ) {

1668  "ID2S-Split-Info without skeleton Seq-entry"

);

1678  "CProcessor_ID2: parsed Seq-entry"

,

1683  result

.SetAndSaveBlobState(blob_id, blob_state);

1694  result

.GetAddWGSMasterDescr() ) {

1700  "CProcessor_ID2: attached entry"

,

1709  if

( with_skeleton ) {

1715

writer, split_version,

data

);

1724

writer, split_version,

data

, *skel);

1735  "ID2S-Chunk in main reply"

);

1749  "CProcessor_ID2: parsed split chunk"

,

1761  "CProcessor_ID2: attached chunk"

,

1775  "invalid data type: "

<<

data

.GetData_type());

1789

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

1814

obj_stream <<

data

;

1827  data

.SetData_type(

data

.GetData_type()+1);

1846

stream.write(&(**it)[0], (*it)->size());

1858  switch

(

data

.GetData_format() ) {

1870  "CId2Reader::x_ReadData(): unknown data format"

);

1872

unique_ptr<IReader> reader(

new

COSSReader(

data

.GetData()));

1873

unique_ptr<CNcbiIstream> stream;

1874  switch

(

data

.GetData_compression() ) {

1882

stream.reset(

new CRStream

(reader.release(),

1890  "CId2Reader::x_ReadData(): unknown data compression"

);

1892  if

( !stream.get() ) {

1893

stream.reset(

new CRStream

(reader.release(),

1896

unique_ptr<CObjectIStream>

in

;

1898  return in

.release();

1907  switch

(

data

.GetData_type() ) {

1909  if

(

object

.GetTypeInfo() != CSeq_entry::GetTypeInfo() ) {

1911  "CId2Reader::x_ReadData(): unexpected Seq-entry"

);

1915  if

(

object

.GetTypeInfo() != CID2S_Split_Info::GetTypeInfo() ) {

1917  "CId2Reader::x_ReadData(): unexpected ID2S-Split-Info"

);

1921  if

(

object

.GetTypeInfo() != CID2S_Chunk::GetTypeInfo() ) {

1923  "CId2Reader::x_ReadData(): unexpected ID2S-Chunk"

);

1928  "CId2Reader::x_ReadData(): unknown data type"

);

1933  in

->Read(

object

);

1934

data_size += size_t(

in

->GetStreamPos());

1945  switch

(

data

.GetData_type() ) {

1947  type

= CSeq_entry::GetTypeInfo();

1950  type

= CID2S_Split_Info::GetTypeInfo();

1953  type

= CID2S_Chunk::GetTypeInfo();

2003

blob_state = obj_stream.

ReadInt4

();

2004

split_version = obj_stream.

ReadInt4

();

2005

obj_stream >> split_data;

2009  "CProcessor_ID2_Split: read skel"

,

2014

split_data, split_version);

2028

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

2055

obj_stream <<

split

;

2099

blob_state = obj_stream.

ReadInt4

();

2100

split_version = obj_stream.

ReadInt4

();

2101

obj_stream >> split_data;

2102

obj_stream >> skel_data;

2106  "CProcessor_ID2AndSkel: read skel"

,

2111

split_data, split_version,

ConstRef

(&skel_data));

2126

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

2156

obj_stream <<

split

;

2232  "CProcessor_ExtAnnot: " 2233  "bad blob "

<<blob_id<<

'/'

<<chunk_id);

2239  "CProcessor_ExtAnnot: " 2240  "double load of "

<<blob_id<<

'/'

<<chunk_id);

2245

vector<SAnnotTypeSelector> more_types;

2251

db_name =

"Annot:SNP"

;

2256

db_name =

"Annot:SNP graph"

;

2262

db_name =

"Annot:CDD"

;

2267

db_name =

"Annot:MGC"

;

2272

db_name =

"Annot:HPRD"

;

2277

db_name =

"Annot:STS"

;

2282

db_name =

"Annot:tRNA"

;

2288

db_name =

"Annot:microRNA"

;

2293

db_name =

"Annot:Exon"

;

2296  _ASSERT

(0 &&

"unknown annot type"

);

2313  ITERATE

( vector<SAnnotTypeSelector>, it, more_types ) {

2327

(OpenStream(writer,

result

, blob_id, chunk_id,

this

));

2372  "CProcessor_AnnotInfo: " 2373  "double load of "

<<blob_id);

2378  info

.GetAnnotInfo()->GetAnnotInfo();

2389

vector<SAnnotTypeSelector>

types

;

2399  int

feat_type = finfo.

GetType

();

2400  if

( feat_type == 0 ) {

2425  if

(

names

.size() == 1 ) {

2445

m_StatType(stat_type), m_Descr(descr),

2446

m_Blob_id(blob_id), m_ChunkId(chunk_id)

2449  bool

IsDone(

void

) {

2455  string

GetErrMsg(

void

)

const

{

2462  string

GetStatisticsDescription(

void

)

const 2465  str

<< m_Descr <<

' '

<< m_Blob_id;

2466  if

( m_ChunkId >= 0 && m_ChunkId <

kMax_Int

)

2467  str

<<

'.'

<< m_ChunkId;

2472  const string

m_Descr;

2486

stat_type, descr, blob_id);

2499

stat_type, descr, blob_id, chunk_id);

User-defined methods of the data storage class.

void SetNamed(const string &name)

const string & GetName(void) const

Class holding information about root of non-modifiable object hierarchy Do not use it directly.

vector< CConstRef< CID2S_Seq_annot_Info > > TAnnotInfo

TSatKey GetSatKey() const

TSubSat GetSubSat() const

@ID1server_back.hpp User-defined methods of the data storage class.

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

bool IsLoadedChunk(void) const

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

CTSE_Split_Info & GetSplitInfo(void)

CTSE_Chunk_Info & GetTSE_Chunk_Info(void)

bool IsLoaded(void) const

CTSE_LoadLock & GetTSE_LoadLock(void)

TBlobState GetBlobState(void) const

Data loader exceptions, used by GenBank loader.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

list< TOctetString * > TOctetStringSequence

virtual ERW_Result Flush(void)

Flush pending data (if any) down to the output device.

COSSWriter(TOctetStringSequence &out)

TOctetStringSequence & m_Output

vector< char > TOctetString

virtual ERW_Result Write(const void *buffer, size_t count, size_t *written)

Write up to "count" bytes from the buffer pointed to by the "buf" argument onto the output device.

CObjectIStreamAsnBinary –.

CObjectOStreamAsnBinary –.

static bool TryStringPack(void)

CProcessor_AnnotInfo(CReadDispatcher &dispatcher)

~CProcessor_AnnotInfo(void)

TMagic GetMagic(void) const

EType GetType(void) const

static void LoadBlob(CReaderRequestResult &result, const CBlob_Info &blob_info)

TMagic GetMagic(void) const

CProcessor_ExtAnnot(CReadDispatcher &dispatcher)

void Process(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id) const

EType GetType(void) const

~CProcessor_ExtAnnot(void)

void ProcessStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const

static bool IsExtAnnot(const TBlobId &blob_id)

EType GetType(void) const

~CProcessor_ID1_SNP(void)

TMagic GetMagic(void) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

CProcessor_ID1_SNP(CReadDispatcher &dispatcher)

TSeqEntryInfo GetSeq_entry(CReaderRequestResult &result, const TBlobId &blob_id, CID1server_back &reply) const

CProcessor_ID1(CReadDispatcher &dispatcher)

TBlobVersion GetVersion(const CID1server_back &reply) const

TMagic GetMagic(void) const

void SaveBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CWriter *writer, CRef< CByteSource > byte_source) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

pair< CRef< CSeq_entry >, int > TSeqEntryInfo

EType GetType(void) const

~CProcessor_ID2AndSkel(void)

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

CProcessor_ID2AndSkel(CReadDispatcher &dispatcher)

void SaveDataAndSkel(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state, TChunkId chunk_id, CWriter *writer, TSplitVersion split_version, const CID2_Reply_Data &split_data, const CID2_Reply_Data &skel_data) const

TMagic GetMagic(void) const

EType GetType(void) const

CProcessor_ID2_Split(CReadDispatcher &dispatcher)

void SaveSplitData(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state, TChunkId chunk_id, CWriter *writer, TSplitVersion split_version, const CID2_Reply_Data &split_data) const

~CProcessor_ID2_Split(void)

TMagic GetMagic(void) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

EType GetType(void) const

static CObjectIStream * x_OpenDataStream(const CID2_Reply_Data &data)

static void x_FixDataFormat(CID2_Reply_Data &data)

EType GetType(void) const

void SaveData(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state, TChunkId chunk_id, CWriter *writer, const CID2_Reply_Data &data) const

TMagic GetMagic(void) const

static void x_ReadData(const CID2_Reply_Data &data, const CObjectInfo &object, size_t &data_size)

CProcessor_ID2(CReadDispatcher &dispatcher)

static void DumpDataAsText(const CID2_Reply_Data &data, CNcbiOstream &out)

void ProcessData(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state, TChunkId chunk_id, const CID2_Reply_Data &data, TSplitVersion split_version=0, const CID2_Reply_Data *skel=0) const

static void x_FixCompression(CID2_Reply_Data &data)

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

TMagic GetMagic(void) const

CProcessor_SE_SNP(CReadDispatcher &dispatcher)

EType GetType(void) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

EType GetType(void) const

CWriter * x_GetWriterToSaveBlob(CReaderRequestResult &result, const CBlob_id &blob_id, CLoadLockSetter &setter, const char *processor_name) const

CProcessor_SE(CReadDispatcher &dispatcher)

TMagic GetMagic(void) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

~CProcessor_St_SE_SNPT(void)

EType GetType(void) const

void ProcessStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const

TMagic GetMagic(void) const

void SaveSNPBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CWriter *writer, const CSeq_entry &seq_entry, TBlobState blob_state, const CTSE_SetObjectInfo &set_info) const

CProcessor_St_SE_SNPT(CReadDispatcher &dispatcher)

CProcessor_St_SE(CReadDispatcher &dispatcher)

void WriteBlobState(CNcbiOstream &stream, TBlobState blob_state) const

TBlobState ReadBlobState(CNcbiIstream &stream) const

TMagic GetMagic(void) const

list< TOctetString * > TOctetStringSequence

void SaveBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, TBlobState blob_state, CWriter *writer, CRef< CByteSource > byte_source) const

void SaveNoBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, TBlobState blob_state, CWriter *writer) const

void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

EType GetType(void) const

CWriter * GetWriter(const CReaderRequestResult &result) const

static bool TrySNPTable(void)

virtual void ProcessObjStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CObjectIStream &obj_stream) const

static bool TryStringPack(void)

static void OffsetAllGisToOM(CBeginInfo obj, CTSE_SetObjectInfo *set_info=0)

static int CollectStatistics(void)

@ eType_St_Seq_entry_SNPT

static TGi ConvertGiToOM(TGi gi)

static void RegisterAllProcessors(CReadDispatcher &dispatcher)

virtual void ProcessStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const

static bool TrySNPSplit(void)

static void OffsetAllGis(CBeginInfo obj, TIntId gi_offset)

CProcessor(CReadDispatcher &dispatcher)

virtual ~CProcessor(void)

void ProcessBlobFromID2Data(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, const CID2_Reply_Data &data) const

static void SetSeqEntryReadHooks(CObjectIStream &in)

static TIntId GetGiOffset(void)

static void OffsetGi(TGi &gi, TIntId gi_offset)

static bool OffsetId(CSeq_id &id, TIntId gi_offset)

static void LogStat(CReaderRequestResultRecursion &recursion, const CBlob_id &blob_id, CGBRequestStatistics::EStatType stat_type, const char *descr, double size)

static void SetSNPReadHooks(CObjectIStream &in)

CReadDispatcher * m_Dispatcher

static void OffsetAllGisFromOM(CBeginInfo obj)

Note about the "buf_size" parameter for streams in this API.

static void LogStat(CReadDispatcherCommand &command, CReaderRequestResultRecursion &recursion)

const CProcessor & GetProcessor(CProcessor::EType type) const

void InsertProcessor(CRef< CProcessor > processor)

CWriter * GetWriter(const CReaderRequestResult &result, CWriter::EType type) const

CReaderRequestResult & GetResult(void) const

@ eSubtype_misc_difference

static void Write(CNcbiOstream &stream, const CSeq_annot_SNP_Info &snp_info)

static void Read(CNcbiIstream &stream, CSeq_annot_SNP_Info &snp_info)

static void Parse(CObjectIStream &in, CSeq_entry &tse, CTSE_SetObjectInfo &set_info)

static void Attach(CTSE_Info &tse, const CID2S_Split_Info &split)

static void x_ParseLocation(TLocationSet &vec, const CID2S_Seq_loc &loc)

static void Load(CTSE_Chunk_Info &chunk, const CID2S_Chunk &data)

Guard class for CObjectIStream::StartDelayBuffer/EndDelayBuffer.

vector< TLocation > TLocationSet

void x_AddBioseqPlace(TBioseq_setId id)

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

void x_AddBioseqId(const TBioseqId &id)

void SetName(const CAnnotName &name)

CTSE_Split_Info & GetSplitInfo(void)

bool x_NeedsDelayedMainChunk(void) const

TSeq_annot_InfoMap m_Seq_annot_InfoMap

void AddChunk(CTSE_Chunk_Info &chunk_info)

void SetSplitVersion(TSplitVersion version)

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

Template class for iteration on objects of class C.

static void AddWGSMaster(CTSE_LoadLock &lock)

Writer-based output stream.

virtual CRef< CBlobStream > OpenBlobStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, const CProcessor &processor)=0

static void WriteBytes(CNcbiOstream &stream, CRef< CByteSource > bs)

CZipStreamCompressor – zlib based compression stream processor.

CZipStreamDecompressor – zlib based decompression stream processor.

A very basic data-read interface.

A very basic data-write interface.

const unsigned char kMagic[2]

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

static const char * str(char *buf, int n)

static const struct type types[]

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

@ eTakeOwnership

An object can take ownership of another.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

void Info(CExceptionArgs_Base &args)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

ESerialDataFormat

Data file format.

@ eSerialSkipUnknown_Yes

do skip

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

CRef< CByteSource > EndDelayBuffer(void)

Redirect call to protected CObjectIStream After this call guarding is finished.

TFlags SetFlags(TFlags flags)

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

virtual void WriteInt4(Int4 data)=0

CNcbiStreampos GetStreamPos(void) const

Get the current stream position.

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

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

void StartDelayBuffer(CObjectIStream &istr)

Start deley buffer collection on a given CObjectIStream object.

virtual Int4 ReadInt4(void)

void Copy(const CObjectTypeInfo &type)

Copy data.

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-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.

virtual CRef< CByteSourceReader > Open(void)=0

ERW_Result

Result codes for I/O operations.

Int8 NcbiStreamposToInt8(NCBI_NS_STD::char_traits< char >::pos_type stream_pos)

Convert stream position to 64-bit int.

virtual ERW_Result PendingCount(size_t *count)=0

Via parameter "count" (which is guaranteed to be supplied non-NULL) return the number of bytes that a...

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

virtual ERW_Result Read(void *buf, size_t count, size_t *bytes_read=0)=0

Read as many as "count" bytes into a buffer pointed to by the "buf" argument.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

NCBI_NS_STD::string::size_type SIZE_TYPE

static TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

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

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

const TGotblobinfo & GetGotblobinfo(void) const

Get the variant data.

TBlob_state GetBlob_state(void) const

Get the Blob_state member data.

TGetgihist & SetGetgihist(void)

Select the variant.

TGetgirev & SetGetgirev(void)

Select the variant.

TGotgi & SetGotgi(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TError GetError(void) const

Get the variant data.

bool IsGotgi(void) const

Check if variant Gotgi is selected.

const TGotsewithinfo & GetGotsewithinfo(void) const

Get the variant data.

TGetgistate & SetGetgistate(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

void SetBlob(TBlob &value)

Assign a value to Blob data member.

TGotseqentry & SetGotseqentry(void)

Select the variant.

TGotdeadseqentry & SetGotdeadseqentry(void)

Select the variant.

TGetseqidsfromgi & SetGetseqidsfromgi(void)

Select the variant.

TGotsewithinfo & SetGotsewithinfo(void)

Select the variant.

const TBlob_info & GetBlob_info(void) const

Get the Blob_info member data.

bool IsSetBlob(void) const

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

@ e_Getgihist

get an historical list of gis

@ e_Getgirev

get a revision history of gi

@ e_Getseqidsfromgi

get all Seq-ids of given gi

@ e_Getgistate

get a state of gi

TData & SetData(void)

Assign a value to Data data member.

list< vector< char > * > TData

@ eData_type_id2s_split_info

@ eData_compression_nlmzip

@ eData_format_asn_binary

list< CRef< C_E > > Tdata

const TSubtypes & GetSubtypes(void) const

Get the Subtypes member data.

bool IsSetSkeleton(void) const

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

const TSeq_loc & GetSeq_loc(void) const

Get the Seq_loc member data.

bool IsSetGraph(void) const

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

list< CRef< CID2S_Feat_type_Info > > TFeat

bool IsSetAlign(void) const

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

bool IsSetSubtypes(void) const

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

void SetSkeleton(TSkeleton &value)

Assign a value to Skeleton data member.

bool IsWhole_gi(void) const

Check if variant Whole_gi is selected.

const TName & GetName(void) const

Get the Name member data.

const TFeat & GetFeat(void) const

Get the Feat member data.

bool IsSetFeat(void) const

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

TWhole_gi & SetWhole_gi(void)

Select the variant.

TType GetType(void) const

Get the Type member data.

E_Choice

Choice variants.

TGeneral & SetGeneral(void)

Select the variant.

@ e_General

for other databases

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

string Execute(const string &cmmd, const vector< string > &args, const string &data=kEmptyStr)

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

string s_Value(TValue value)

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

static bool s_UseMemoryPool(void)

NCBI_PARAM_DEF_EX(bool, GENBANK, SNP_PACK_STRINGS, true, eParam_NoThread, GENBANK_SNP_PACK_STRINGS)

static bool s_CacheRecompress(void)

static bool s_CanBeWGSBlob(const CBlob_id &blob_id)

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Reader-writer based streams.

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