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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader__id2__base_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/reader_id2_base.cpp Source File

71 #define NCBI_USE_ERRCODE_X Objtools_Rd_Id2Base 79

{

""

, objects::CSeq_id::eSNPScaleLimit_Default},

80

{

"Unit"

, objects::CSeq_id::eSNPScaleLimit_Unit},

81

{

"Contig"

, objects::CSeq_id::eSNPScaleLimit_Contig},

82

{

"Supercontig"

, objects::CSeq_id::eSNPScaleLimit_Supercontig},

83

{

"Chromosome"

, objects::CSeq_id::eSNPScaleLimit_Chromosome},

87

objects::CSeq_id::eSNPScaleLimit_Default,

103 # define DEFAULT_DEBUG_LEVEL CId2ReaderBase::eTraceError 105 # define DEFAULT_DEBUG_LEVEL 0 136  return

TGenbankVdbSnpParam::GetDefault();

142  return

TGenbankVdbSnpParam::SetDefault(enabled);

148  return

TGenbankVdbWgsParam::GetDefault();

154  return

TGenbankVdbWgsParam::SetDefault(enabled);

160  return

TGenbankVdbCddParam::GetDefault();

166  return

TGenbankVdbCddParam::SetDefault(enabled);

172  return

TID2SNP_Scale_Limit::GetDefault();

178

TID2SNP_Scale_Limit::SetDefault(

value

);

195  return

(

size_t

)

s_Value

->Get();

202  return

(

size_t

)

s_Value

->Get();

210  return

max_request_size == 1;

218  return

max_request_size > 0;

249

: m_RequestSerialNumber(1),

252

vector<string> proc_list;

253  string

proc_param =

NCBI_PARAM_TYPE

(GENBANK, ID2_PROCESSOR)::GetDefault();

255  ITERATE

( vector<string>, it, proc_list ) {

256  const string

& proc_name = *it;

260

CreateInstance(proc_name);

264  "cannot load ID2 processor "

<<proc_name<<

": "

<<exc);

266  if

(

info

.processor ) {

267  info

.context =

info

.processor->CreateContext();

273

packet.

Set

().push_back(

Ref

(&req));

275  info

.processor->ProcessPacket(

info

.context, packet, replies);

293 #define MConnFormat MSerial_AsnBinary 300

get_blob_id.

SetSeq_id

().SetSeq_id().SetSeq_id().Assign(seq_id);

321  result

.GetLoadedBlob_ids(idh, loaded_blob_ids);

322  if

( loaded_blob_ids.empty() ) {

325

CID2_Request_Get_Blob_Info::C_Blob_id::C_Resolve::TExclude_blobs&

327

get_blob_info.

SetBlob_id

().SetResolve().SetExclude_blobs();

331

exclude_blobs.push_back(blob_id);

360  if

( ids.IsLoaded() ) {

367

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

384

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

406

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

432

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

459

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

486

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

513

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

541

get_id.SetSeq_id().SetSeq_id().Assign(*seq_id.

GetSeqId

());

559  if

( max_request_size <= 1 ) {

563  size_t count

= ids.size();

565  size_t

packet_start = 0;

567  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

572  if

( lock.IsLoaded() ) {

574  if

(

data

.IsFound() ) {

575

ret[

i

] =

data

.Get();

584

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

586  if

( packet.

Set

().empty() ) {

589

packet.

Set

().push_back(req);

590  if

( packet.

Set

().size() == max_request_size ) {

593  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

598  if

( lock.IsLoaded() ) {

600  if

(

data

.IsFound() ) {

601

ret[

i

] =

data

.Get();

607

packet.

Set

().clear();

611  if

( !packet.

Set

().empty() ) {

614  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

619  if

( lock.IsLoaded() ) {

621  if

(

data

.IsFound() ) {

622

ret[

i

] =

data

.Get();

638  if

( max_request_size <= 1 ) {

642  size_t count

= ids.size();

644  size_t

packet_start = 0;

646  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

663

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

665  if

( packet.

Set

().empty() ) {

668

packet.

Set

().push_back(req);

669  if

( packet.

Set

().size() == max_request_size ) {

672  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

686

packet.

Set

().clear();

690  if

( !packet.

Set

().empty() ) {

693  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

717  if

( max_request_size <= 1 ) {

721  size_t count

= ids.size();

723  size_t

packet_start = 0;

725  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

742

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

744  if

( packet.

Set

().empty() ) {

747

packet.

Set

().push_back(req);

748  if

( packet.

Set

().size() == max_request_size ) {

751  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

765

packet.

Set

().clear();

769  if

( !packet.

Set

().empty() ) {

772  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

796  if

( max_request_size <= 1 ) {

800  size_t count

= ids.size();

802  size_t

packet_start = 0;

804  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

818

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

825  if

( packet.

Set

().empty() ) {

828

packet.

Set

().push_back(req);

829  if

( packet.

Set

().size() == max_request_size ) {

832  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

845  if

( ids_lock.IsLoaded() ) {

848

ids_lock.GetExpirationTime());

854

packet.

Set

().clear();

858  if

( !packet.

Set

().empty() ) {

861  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

874  if

( ids_lock.IsLoaded() ) {

877

ids_lock.GetExpirationTime());

893  if

( max_request_size <= 1 ||

898  size_t count

= ids.size();

900  size_t

packet_start = 0;

902  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

919

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

921  if

( packet.

Set

().empty() ) {

924

packet.

Set

().push_back(req);

925  if

( packet.

Set

().size() == max_request_size ) {

928  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

942

packet.

Set

().clear();

946  if

( !packet.

Set

().empty() ) {

949  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

974  if

( max_request_size <= 1 ||

979  size_t count

= ids.size();

981  size_t

packet_start = 0;

983  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

993  if

(

hash

.hash_known ) {

994

ret[

i

] =

hash

.hash;

999  else if

( !

hash

.sequence_found ) {

1008

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

1010  if

( packet.

Set

().empty() ) {

1013

packet.

Set

().push_back(req);

1014  if

( packet.

Set

().size() == max_request_size ) {

1017  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1024  if

(

hash

.hash_known ) {

1025

ret[

i

] =

hash

.hash;

1026

loaded[

i

] =

true

;

1030  else if

( !

hash

.sequence_found ) {

1039

packet.

Set

().clear();

1043  if

( !packet.

Set

().empty() ) {

1046  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1052  if

(

hash

.hash_known ) {

1053

ret[

i

] =

hash

.hash;

1054

loaded[

i

] =

true

;

1058  else if

( !

hash

.sequence_found ) {

1076  if

( max_request_size <= 1 ||

1081  size_t count

= ids.size();

1083  size_t

packet_start = 0;

1085  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

1095

loaded[

i

] =

true

;

1102

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

1105  if

( packet.

Set

().empty() ) {

1108

packet.

Set

().push_back(req);

1109  if

( packet.

Set

().size() == max_request_size ) {

1112  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1119

loaded[

i

] =

true

;

1126

packet.

Set

().clear();

1130  if

( !packet.

Set

().empty() ) {

1133  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1140

loaded[

i

] =

true

;

1157  if

( max_request_size <= 1 ||

1162  size_t count

= ids.size();

1164  size_t

packet_start = 0;

1166  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

1178

loaded[

i

] =

true

;

1186

get_id.SetSeq_id().SetSeq_id().Assign(*ids[

i

].

GetSeqId

());

1189  if

( packet.

Set

().empty() ) {

1192

packet.

Set

().push_back(req);

1193  if

( packet.

Set

().size() == max_request_size ) {

1196  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1205

loaded[

i

] =

true

;

1213

packet.

Set

().clear();

1217  if

( !packet.

Set

().empty() ) {

1220  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1229

loaded[

i

] =

true

;

1247  if

( max_request_size <= 1 ) {

1251  size_t count

= ids.size();

1253  size_t

packet_start = 0;

1255  for

(

size_t i

= 0;

i

<

count

; ++

i

) {

1262  if

( packet.

Set

().empty() ) {

1265

packet.

Set

().push_back(req);

1266  if

( packet.

Set

().size() == max_request_size ) {

1269  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1272

packet.

Set

().clear();

1276  if

( !packet.

Set

().empty() ) {

1279  for

(

size_t i

= packet_start;

i

<

count

; ++

i

) {

1293  if

( ids.IsLoaded() ) {

1303

srcs.push_back(it->first);

1304  if

(it->first ==

"SNP"

) {

1311

param->SetName(

"snp:scale-limit"

);

1313

req.

SetParams

().Set().push_back(param);

1338  ERR_POST_X

(5,

"ExtAnnot blob state is not loaded: "

<<blob_id);

1339  result

.SetLoadedBlobState(blob_id, 0);

1361  ERR_POST_X

(9,

"ExtAnnot blob version is not loaded: "

<<blob_id);

1362  result

.SetLoadedBlobVersion(blob_id, 0);

1375  if

( !ids.IsLoaded() ) {

1383  if

( ids.IsLoaded() ) {

1398  return

ids.IsLoaded();

1414  if

( !

info

.Matches(

mask

, sel) ) {

1422  if

(

info

.IsSetAnnotInfo() ) {

1437

packet.

Set

().push_back(req);

1443

packet.

Get

().size() >= max_request_size ) {

1445

packet.

Set

().clear();

1448  if

( !packet.

Get

().empty() ) {

1498  ERR_POST_X

(2,

"ExtAnnot chunk is not loaded: "

<<blob_id);

1520

vector<TChunkId>& chunks,

1529  ERR_POST_X

(3,

"ExtAnnot chunk is not loaded: "

<< blob_id);

1534

packet.

Set

().clear();

1543  for

(

auto

& blob_chunks : chunk_ids ) {

1546

packet.

Set

().clear();

1555  if

( chunk_ids.size() == 1 ) {

1578

vector<TChunkId> ext_chunks;

1590

packet.

Set

().push_back(ext_req);

1591

ext_chunks.push_back(*

id

);

1593

packet.

Get

().size() >= max_request_size ) {

1602

chunks.size() >= max_request_size ) {

1609  if

( !chunks.empty() ) {

1611

packet.

Get

().size() + chunks.size() > max_request_size ) {

1617

packet.

Set

().push_back(chunks_req);

1620  if

( !packet.

Get

().empty() ) {

1637  size_t

requested_count = 0;

1638  for

(

auto

& blob_chunks : chunk_ids ) {

1639  const CBlob_id

& blob_id = blob_chunks.first;

1644  for

(

auto

chunk_id : blob_chunks.second ) {

1656

packet.

Set

().push_back(req);

1657

requested_chunks.push_back(make_pair(blob_id,

TChunkIds

()));

1661  if

( !chunks_list ) {

1670

packet.

Set

().push_back(req);

1671

chunks_list = &get_chunks.

SetChunks

();

1672

requested_chunks.push_back(make_pair(blob_id,

TChunkIds

()));

1677

requested_chunks.back().second.push_back(chunk_id);

1680

requested_count >= max_request_size ) {

1684

requested_count = 0;

1690  if

( requested_count ) {

1693

requested_count = 0;

1704  for

(

auto

&

info

: blob_infos ) {

1711  if

(

info

.IsSetAnnotInfo() ) {

1726

packet.

Set

().push_back(req);

1731

packet.

Get

().size() >= max_request_size ) {

1733

packet.

Set

().clear();

1737  if

( !packet.

Get

().empty() ) {

1757  if

( ids.IsLoaded() ) {

1763

packet.

Set

().push_back(req);

1765

packet.

Get

().size() >= max_request_size ) {

1768

packet.

Set

().clear();

1771  if

( !packet.

Get

().empty() ) {

1786  bool

loaded_blob_ids =

false

;

1787  size_t

processed_requests = 0;

1792

loaded_blob_ids =

true

;

1798  if

( !loaded_blob_ids &&

1803

loaded_blob_ids =

true

;

1806  if

( ids && ids.IsLoaded() ) {

1819  if

( !load_blob_ids.

insert

(blob_id).second ) {

1827

packet.

Set

().push_back(req);

1829

packet.

Get

().size() >= max_request_size ) {

1830

processed_requests += packet.

Set

().size();

1832

packet.

Set

().clear();

1844

packet.

Set

().push_back(req);

1846

packet.

Get

().size() >= max_request_size ) {

1847

processed_requests += packet.

Set

().size();

1849

packet.

Set

().clear();

1853  if

( !packet.

Get

().empty() ) {

1854

processed_requests += packet.

Get

().size();

1857  if

( !processed_requests && !loaded_blob_ids ) {

1869

packet.

Set

().push_back(

Ref

(&req));

1899

unique_ptr<CReaderAllocatedConnection>

conn

;

1925

param->SetName(

"log:client_name"

);

1927

request.

SetParams

().Set().push_back(param);

1930

param->SetName(

"id2:allow"

);

1932

param->SetValue().push_back(

"*.blob-state"

);

1935

param->SetValue().push_back(

"vdb-wgs"

);

1939

param->SetValue().push_back(

"vdb-snp"

);

1943

param->SetValue().push_back(

"vdb-cdd"

);

1945

request.

SetParams

().Set().push_back(param);

1950

param->SetName(

"snp:scale-limit"

);

1952

request.

SetParams

().Set().push_back(param);

1958

param->SetName(

"session_id"

);

1960

request.

SetParams

().Set().push_back(param);

1964

param->SetName(

"log:ncbi_phid"

);

1966

request.

SetParams

().Set().push_back(param);

1970

param->SetName(

"log:client_ip"

);

1971

param->SetValue().push_back(rctx.

GetClientIP

());

1972

request.

SetParams

().Set().push_back(param);

1977 #define x_GetReaderName(conn) \ 1978  (x_ConnDescription((conn)).empty()? "CPubseq2Reader"

: "CId2Reader")

1992

s <<

" ID2-Request-Packet"

;

2012  if

( iter && iter->IsSetData() ) {

2014

save.swap(iter->SetData());

2015  size_t size

= 0,

count

= 0, max_chunk = 0;

2018  size_t

chunk = (*i)->size();

2020

max_chunk =

max

(max_chunk, chunk);

2023  "Data: "

<<

size

<<

" bytes in "

<<

2024  count

<<

" chunks with "

<<

2025

max_chunk <<

" bytes in chunk max"

;

2026

save.swap(iter->SetData());

2034

s <<

" ID2-Reply."

;

2040  if

( it->IsSetData() ) {

2045  ERR_POST_X

(1,

"Exception while dumping data: " 2064  "failed to send request: "

+

2069

s <<

"Sent ID2-Request-Packet."

;

2078

s <<

"Receiving ID2-Reply..."

;

2086  "reply deserialization failed: "

+

2102  state

.stages.reserve(proc_count);

2103  for

(

size_t i

= 0;

i

< proc_count; ++

i

) {

2104  if

( packet.

Get

().empty() ) {

2107  state

.stages.resize(

i

+1);

2114  for

(

auto

& it : stage.

replies

) {

2120  if

( packet.

Get

().empty() ) {

2128

s <<

"Sending ID2-Request-Packet..."

;

2133

s <<

"Sent ID2-Request-Packet."

;

2138  "failed to send request: "

+

2146  if

( pos <

state

.stages.size() ) {

2149  while

( stage.

replies

.empty() ) {

2154  x_DumpReply

(0, *reply,

"Filtered by processor"

);

2155  for

(

auto

& it : stage.

replies

) {

2171

s <<

"Receiving ID2-Reply..."

;

2179  "reply deserialization failed: "

+

2183  if

( reply->IsSetDiscard() ) {

2204  if

( !packet.

Get

().empty() ) {

2209  for

(

auto

&

i

: packet.

Get

() ) {

2210  info

.requests.push_back(

i

.GetPointer());

2212  info

.request_count =

static_cast<int>

(

info

.requests.size());

2213  info

.remaining_count =

info

.request_count;

2214  int

end_serial_num =

2216  while

( end_serial_num <=

info

.request_count ) {

2222  if

( num <=

info

.request_count ) {

2229  info

.start_serial_num = end_serial_num -

info

.request_count;

2231  int

cur_serial_num =

info

.start_serial_num;

2233

(*it)->SetSerial_number(cur_serial_num++);

2256

descr =

" (processor)"

;

2264  "CId2ReaderBase: connection timed out"

<<descr);

2268  "CId2ReaderBase: connection failed"

<<descr);

2272  "CId2ReaderBase: failed command"

<<descr);

2276  ERR_POST_X

(8,

"CId2ReaderBase: bad reply serial number: "

<<descr);

2280  "CId2ReaderBase: bad reply serial number: "

<<descr);

2291  info

.requests[num] = 0;

2292

--

info

.remaining_count;

2306

vector<SId2LoadedSet> loaded_sets(packet_info.

request_count

);

2327  "CId2ReaderBase: failed to process reply: "

+

2336  if

(

state

.conn ) {

2340  catch

( exception&

) {

2345

(reply->IsSetSerial_number() ||

2346

reply->IsSetParams() ||

2347

reply->IsSetError() ||

2348

reply->IsSetEnd_of_reply() ||

2349

reply->IsSetReply()) ) {

2353  catch

( exception&

) {

2359  if

(

state

.conn ) {

2360  state

.conn->Release();

2390  data

.m_Seq_ids.clear();

2393  if

( ids.IsLoaded() ) {

2396  int state

= it->second.first;

2400  CBlob_Info

blob_info(blob_id, it2->second.m_ContentMask);

2405  if

( !blob_annot_info ) {

2410

blob_annot_info->AddNamedAnnotName(annot_info.

GetName

());

2413

annot_info.

IsSetGraph

() && ainfos.size() == 1 &&

2418

s <<

"Adding zoom tracks for " 2421  for

(

int

zoom = 10; zoom < 1000000; zoom *= 10 ) {

2424

zoom_info->ResetFeat();

2425

zoom_info->ResetAlign();

2427

blob_annot_info->AddAnnotInfo(*zoom_info);

2439

blob_annot_info->AddAnnotInfo(annot_info);

2442  if

( blob_annot_info &&

2443

!(blob_annot_info->GetAnnotInfo().empty() &&

2444

blob_annot_info->GetNamedAnnotNames().empty()) ) {

2447

blob_ids.push_back(blob_info);

2459  const char

* marker1,

2460  const char

* marker2)

2462  if

( !

error

.IsSetMessage() ) {

2466  if

( error_flags & test_flag ) {

2471  if

( pos ==

NPOS

) {

2480

error_flags |= test_flag;

2489  switch

(

error

.GetSeverity() ) {

2492  if

(

error

.IsSetMessage() ) {

2493  const string

&

msg

=

error

.GetMessage();

2494  if

(

msg

.find(

"PTIS_FAILURE"

) !=

NPOS

) {

2510  if

(

error

.IsSetMessage() ) {

2532  if

(

error

.IsSetRetry_delay() ) {

2543  switch

(

error

.GetSeverity() ) {

2546  if

(

error

.IsSetMessage() ) {

2559  "Unknown satellite number 20 for bioseq info"

);

2579  if

(

error

.IsSetMessage() ) {

2674

*errors_ptr = errors;

2706  "CId2ReaderBase: connection failed"

);

2709  ERR_POST_X

(17,

"CId2ReaderBase: failed command reply: "

<<

2713  "CId2ReaderBase: failed command"

);

2716  auto

& reply = main_reply.

GetReply

();

2717  switch

( reply.Which() ) {

2720

reply.GetGet_seq_id().GetRequest(),

2721

&reply.GetGet_seq_id());

2725

reply.GetGet_blob_id());

2729

reply.GetGet_blob_seq_ids());

2733

reply.GetGet_blob());

2737

reply.GetGet_split_info());

2741

reply.GetGet_chunk());

2759  auto

& request = main_request.

GetRequest

();

2760  switch

( request.Which() ) {

2765  if

( request.GetGet_blob_id().IsSetSeq_id() ) {

2766  auto

& req_id = request.GetGet_blob_id().GetSeq_id().GetSeq_id();

2767  if

( req_id.IsSeq_id() ) {

2774  if

( request.GetGet_blob_info().GetBlob_id().IsResolve() ) {

2775  auto

& req_id = request.GetGet_blob_info().GetBlob_id().GetResolve().GetRequest().GetSeq_id().GetSeq_id();

2776  if

( req_id.IsSeq_id() ) {

2797  switch

( req_id.

Which

() ) {

2812  if

( !

id

.IsGeneral() ) {

2815  const string

& db =

id

.GetGeneral().GetDb();

2866  bool

got_no_ids =

false

;

2877

got_no_ids = seq_ids.empty();

2891  if

( (**it).IsGi() ) {

2892

ret.

gi

= (**it).GetGi();

2902  if

( (**it).GetTextseq_Id() ) {

2913  if

(

id

.IsGeneral() ) {

2914  const CDbtag

& dbtag =

id

.GetGeneral();

2927  if

(

id

.IsGeneral() ) {

2928  const CDbtag

& dbtag =

id

.GetGeneral();

2944  if

(

id

.IsGeneral() ) {

2945  const CDbtag

& dbtag =

id

.GetGeneral();

2949  hash

.sequence_found =

true

;

2950  hash

.hash_known =

true

;

2961  if

(

id

.IsGeneral() ) {

2962  const CDbtag

& dbtag =

id

.GetGeneral();

2978  if

(

id

.IsGeneral() ) {

2979  const CDbtag

& dbtag =

id

.GetGeneral();

2983  type

.sequence_found =

true

;

2988  if

(

type

.sequence_found || got_no_ids ) {

3012

blob_state =

x_GetBlobState

(blob_id, loaded_set, main_reply, &errors);

3023

ids.first |= blob_state;

3037  if

( obj_id.

IsId

() &&

3057  if

(

info

.IsSetFeat() ) {

3060  if

(

info

.IsSetGraph() ) {

3063  if

(

info

.IsSetAlign() ) {

3126  if

( !blob_version ) {

3145  if

(

data

.GetData().empty() ) {

3147  data

.GetData_type() ==

data

.eData_type_seq_entry ) {

3150  "no data in reply: "

<<blob_id);

3153  ERR_POST_X

(7,

"CId2ReaderBase: ID2-Reply-Get-Blob: " 3154  "no data in reply: "

<<blob_id);

3175  "blob already loaded: "

<<blob_id);

3181  result

.SetAndSaveBlobState(blob_id, blob_state);

3191

.ProcessData(

result

, blob_id, blob_state, chunk_id,

data

);

3212  ERR_POST_X

(11,

"CId2ReaderBase: ID2S-Reply-Get-Split-Info: " 3213  "no data in reply: "

<<blob_id);

3217  if

( !blob_version ) {

3235  ERR_POST_X

(10,

Info

<<

"CId2ReaderBase: ID2S-Reply-Get-Split-Info: " 3236  "blob already loaded: "

<< blob_id);

3259

skel = iter->second;

3264  result

.SetAndSaveBlobState(blob_id, blob_state);

3269

.ProcessData(

result

, blob_id, blob_state, chunk_id,

3285  ERR_POST_X

(14,

"CId2ReaderBase: ID2S-Reply-Get-Chunk: " 3286  "no data in reply: "

<<blob_id);

3291  ERR_POST_X

(13,

"CId2ReaderBase: ID2S-Reply-Get-Chunk: " 3292  "blob is not loaded yet: "

<< blob_id);

ncbi::TMaskedQueryRegions mask

void SetAnnotInfo(CRef< CBlob_Annot_Info > &annot_info)

void SetSubSat(TSubSat v)

TSatKey GetSatKey() const

void SetSatKey(TSatKey v)

TSubSat GetSubSat() const

vector< CRef< CID2_Reply > > TReplies

CID2S_Reply_Get_Chunk –.

CID2S_Reply_Get_Split_Info –.

CID2S_Request_Get_Chunks –.

CID2S_Seq_annot_Info –.

CID2_Get_Blob_Details –.

CID2_Reply_Get_Blob_Id –.

CID2_Reply_Get_Blob_Seq_ids –.

CID2_Reply_Get_Seq_id –.

CID2_Request_Get_Blob_Id –.

CID2_Request_Get_Blob_Info –.

CID2_Request_Get_Seq_id –.

virtual void x_ReceiveReply(TConn conn, CID2_Reply &reply)=0

TBlobState x_GetBlobStateFromID2(const CBlob_id &blob_id, SId2LoadedSet &loaded_set, int id2_state)

bool LoadLabels(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLabels &ret)

void x_SetResolve(CID2_Request_Get_Blob_Id &get_blob_id, const CSeq_id &seq_id)

void x_SendID2Packet(CReaderRequestResult &result, SId2ProcessingState &state, CID2_Request_Packet &packet)

static void SetVDB_CDD_Enabled(bool enabled=true)

bool LoadHashes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, THashes &ret, TKnown &known)

bool LoadSeq_idLabel(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

static bool GetVDB_SNP_Enabled()

bool LoadSeq_idTaxId(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadChunk(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)

void x_AssignSerialNumbers(SId2PacketInfo &info, CID2_Request_Packet &packet)

bool LoadBulkIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TBulkIds &ret)

bool LoadTaxIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTaxIds &ret)

bool LoadChunks(CReaderRequestResult &result, const TBlobId &blob_id, const TChunkIds &chunk_ids)

bool x_LoadSeq_idBlob_idsSet(CReaderRequestResult &result, const TSeqIds &seq_ids)

static TBlobId GetBlobId(const CID2_Blob_Id &blob_id)

bool LoadSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadLengths(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLengths &ret)

void x_ProcessGetBlobSeqIds(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Reply_Get_Blob_Seq_ids &reply)

virtual void x_SendPacket(TConn conn, const CID2_Request_Packet &packet)=0

TErrorFlags x_GetMessageError(const CID2_Error &error)

void x_SetContextData(CID2_Request &request)

TErrorFlags x_GetError(CReaderRequestResult &result, const CID2_Error &error)

void x_DisableProcessors()

void x_ProcessGetChunk(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2S_Reply_Get_Chunk &reply)

bool LoadAccVers(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TIds &ret)

bool LoadTypes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTypes &ret)

bool LoadBlobs(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TContentsMask mask, const SAnnotSelector *sel)

bool x_DoneReply(SId2PacketInfo &info, int num, const CID2_Reply &reply)

atomic< TAvoidRequests > m_AvoidRequest

void x_ProcessGetSplitInfo(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2S_Reply_Get_Split_Info &reply)

static bool GetVDB_CDD_Enabled()

bool LoadBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id)

static int GetDebugLevel(void)

TBlobState x_GetBlobState(const CBlob_id &blob_id, SId2LoadedSet &loaded_set, const CID2_Reply &reply, TErrorFlags *errors_ptr=0)

void x_DumpPacket(TConn conn, const CID2_Request_Packet &packet, const char *msg="Sending")

void x_ProcessGetBlob(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Reply_Get_Blob &reply)

static void SetSNP_Scale_Limit(CSeq_id::ESNPScaleLimit value)

void x_ProcessGetSeqId(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Request_Get_Seq_id &request, const CID2_Reply_Get_Seq_id *reply)

static void SetVDB_SNP_Enabled(bool enabled=true)

void x_SetExclude_blobs(CID2_Request_Get_Blob_Info &get_blob_info, const CSeq_id_Handle &idh, CReaderRequestResult &result)

void x_UpdateLoadedSet(CReaderRequestResult &result, SId2LoadedSet &data, const SAnnotSelector *sel)

void x_SetDetails(CID2_Get_Blob_Details &details, TContentsMask mask)

bool LoadBlobSet(CReaderRequestResult &result, const TSeqIds &seq_ids)

CRef< CID2_Reply > x_ReceiveID2ReplyStage(SId2ProcessingState &state, size_t pos)

void x_ProcessRequest(CReaderRequestResult &result, CID2_Request &req, const SAnnotSelector *sel)

virtual void SetParams(const CReaderParams &params)

void x_ProcessEmptyReply(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Request &main_request)

void x_DumpReply(TConn conn, CID2_Reply &reply, const char *msg="Received")

bool LoadBlobState(CReaderRequestResult &result, const TBlobId &blob_id)

virtual string x_ConnDescription(TConn conn) const =0

bool LoadSequenceType(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

CRef< CID2_Reply > x_ReceiveFromConnection(TConn conn)

virtual void x_EndOfPacket(TConn conn)

static void sx_CheckErrorFlag(const CID2_Error &error, TErrorFlags &error_flags, EErrorFlags test_flag, const char *marker1, const char *marker2=0)

@ fAvoidRequest_for_Seq_id_type

@ fAvoidRequest_nested_get_blob_info

@ fAvoidRequest_for_Seq_id_taxid

@ fAvoidRequest_for_Seq_id_length

@ fAvoidRequest_for_Seq_id_label

@ fAvoidRequest_for_Seq_id_hash

CRef< CID2_Reply > x_ReceiveID2Reply(SId2ProcessingState &state)

CAtomicCounter_WithAutoInit m_RequestSerialNumber

static void SetVDB_WGS_Enabled(bool enabled=true)

bool LoadSequenceLength(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

static bool GetVDB_WGS_Enabled()

void x_ProcessGetBlobId(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Reply_Get_Blob_Id &reply)

void x_ProcessReply(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CID2_Request &main_request)

bool LoadGis(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TGis &ret)

void x_ProcessPacket(CReaderRequestResult &result, CID2_Request_Packet &packet, const SAnnotSelector *sel)

void x_ProcessGetSeqIdSeqId(CReaderRequestResult &result, SId2LoadedSet &loaded_set, const CID2_Reply &main_reply, const CSeq_id_Handle &seq_id, const CID2_Request_Get_Seq_id &request, const CID2_Reply_Get_Seq_id *reply)

@ fError_inactivity_timeout

int x_GetReplyIndex(CReaderRequestResult &result, CConn *conn, SId2PacketInfo &packet, const CID2_Reply &reply)

bool LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

All LoadXxx() methods should return false if there is no requested data in the reader.

bool LoadStates(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TStates &ret)

bool LoadSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

bool LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

static CSeq_id::ESNPScaleLimit GetSNP_Scale_Limit(void)

bool LoadBlob(CReaderRequestResult &result, const TBlobId &blob_id)

void x_SendToConnection(TConn conn, CID2_Request_Packet &packet)

static bool IsFound(const TData &data)

TData GetAccVer(void) const

static const CSeq_id_Handle & GetAcc(const TData &data)

bool IsLoadedAccVer(void) const

TData GetBlob_ids(void) const

bool IsLoadedBlobState(void) const

bool IsLoadedBlobVersion(void) const

void SelectChunk(TChunkId chunk_id)

bool NeedsDelayedMainChunk(void) const

bool IsLoadedChunk(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

bool IsLoadedBlob(void) const

TBlobVersion GetKnownBlobVersion(void) const

bool IsLoadedGi(void) const

static bool IsFound(const TData &data)

static TGi GetGi(const TData &data)

bool IsLoadedHash(void) const

static int GetHash(const TData &data)

bool IsLoadedLabel(void) const

bool SetLoadedLabel(const TData &data)

TData GetLabel(void) const

TData GetLength(void) const

bool IsLoadedLength(void) const

TData GetSeq_ids(void) const

bool IsLoaded(void) const

bool IsLoadedTaxId(void) const

TData GetTaxId(void) const

static bool IsFound(const TData &data)

static CSeq_inst::TMol GetType(const TData &data)

bool IsLoadedType(void) const

Data loader exceptions, used by GenBank loader.

static TPluginManager * Get(void)

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

static bool IsExtAnnot(const TBlobId &blob_id)

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

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

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

static void OffsetAllGisFromOM(CBeginInfo obj)

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

static bool SetBlobState(size_t i, CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TStates &ret)

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

static bool CannotProcess(const CSeq_id_Handle &sih)

bool GetEnableSNP(void) const

bool GetEnableCDD(void) const

bool GetEnableWGS(void) const

bool IsSetEnableCDD(void) const

bool IsSetEnableSNP(void) const

bool IsSetEnableWGS(void) const

vector< CBlob_id > TLoadedBlob_ids

CDataLoader::STypeFound TSequenceType

vector< CSeq_id_Handle > TSeqIds

virtual bool LoadBlobSet(CReaderRequestResult &result, const TSeqIds &seq_ids)

virtual bool LoadHashes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, THashes &ret, TKnown &known)

CReadDispatcher * m_Dispatcher

void SetAndSaveSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceAcc &acc_id) const

virtual bool LoadStates(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TStates &ret)

virtual bool LoadSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

virtual bool LoadSeq_idTaxId(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

CReaderAllocatedConnection CConn

void SetAndSaveNoSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, const CLoadLockGi &gi_lock) const

virtual bool LoadLabels(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLabels &ret)

void SetAndSaveSequenceType(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceType &type) const

virtual bool LoadTypes(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTypes &ret)

void SetAndSaveSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceGi &gi) const

void SetAndSaveBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id, TBlobVersion version) const

vector< CBlob_Info > TBlobIds

virtual bool LoadTaxIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TTaxIds &ret)

void SetAndSaveNoBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, TBlobState blob_state)

virtual bool LoadSequenceType(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void SetAndSaveSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CFixedSeq_ids &seq_ids) const

virtual bool LoadBulkIds(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TBulkIds &ret)

virtual bool LoadSequenceLength(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

virtual bool LoadChunks(CReaderRequestResult &result, const TBlobId &blob_id, const TChunkIds &chunk_ids)

void SetAndSaveSequenceLength(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TSeqPos length) const

void SetAndSaveSeq_idTaxId(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TTaxId taxid) const

vector< TSeqPos > TLengths

vector< pair< TBlobId, TChunkIds > > TBlobChunkIds

virtual bool LoadGis(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TGis &ret)

void SetAndSaveSeq_idLabel(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const string &label) const

virtual bool LoadAccVers(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TIds &ret)

vector< CSeq_inst::EMol > TTypes

virtual bool LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

vector< CSeq_id_Handle > TIds

CDataLoader::SAccVerFound TSequenceAcc

virtual bool LoadSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

CDataLoader::SHashFound TSequenceHash

void SetAndSaveSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, CLoadLockBlobIds &lock, const CLoadLockBlobIds &blob_ids) const

void SetAndSaveSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceHash &hash) const

vector< TChunkId > TChunkIds

virtual bool LoadLengths(CReaderRequestResult &result, const TIds &ids, TLoaded &loaded, TLengths &ret)

virtual bool LoadBlobs(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TContentsMask mask, const SAnnotSelector *sel)

void SetAndSaveNoSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TState state) const

virtual bool LoadSeq_idLabel(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

CDataLoader::SGiFound TSequenceGi

TSplitVersion GetSplitVersion(void) const

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static CS_CONNECTION * conn

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define TAX_ID_FROM(T, value)

@ eTakeOwnership

An object can take ownership of another.

void Set(TValue new_value) THROWS_NONE

Set atomic counter value.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

CDiagContext & GetDiagContext(void)

Get diag context instance.

string GetSessionID(void) const

Session ID.

const string & GetNextSubHitID(CTempString prefix=CTempString())

Get current hit id appended with auto-incremented sub-hit id.

bool IsSetSessionID(void) const

static CRequestContext & GetRequestContext(void)

Shortcut to CDiagContextThreadData::GetThreadData().GetRequestContext()

string GetClientIP(void) const

Client IP/hostname.

bool IsSetHitID(EHitIDSource src=eHitID_Any) const

Check if there's an explicit hit id or the default one.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

bool IsSetClientIP(void) const

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

void Info(CExceptionArgs_Base &args)

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

CConstRef< CSeq_id > GetSeqId(void) const

static const char * GetSNPScaleLimit_Name(ESNPScaleLimit value)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

ESNPScaleLimit

SNP annotation scale limits.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

TSNPScaleLimit GetSNPScaleLimit(void) const

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

Extract optional zoom level suffix from named annotation string.

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

@ eParam_NoThread

Do not use per-thread values.

uint32_t Uint4

4-byte (32-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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Check if a string starts with a specified prefix value.

virtual void Process(SOCK sock)=0

Runs asynchronously (from a separate thread) for each request.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

static const char label[]

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

bool IsSetAnnot_info(void) const

annotation types in this blob annotation are unknown if this field is omitted Check if a value has be...

TVersion GetVersion(void) const

Get the Version member data.

TSat_key GetSat_key(void) const

Get the Sat_key member data.

const TError & GetError(void) const

Get the Error member data.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

bool IsSetBlob_state(void) const

state bits of the blob, 0 or missing means regular live data Check if a value has been assigned to Bl...

void SetSplit_version(TSplit_version value)

Assign a value to Split_version data member.

bool IsSetBlob_state(void) const

state bits of the blob, 0 or missing means regular live data Check if a value has been assigned to Bl...

TSeq_id_type GetSeq_id_type(void) const

Get the Seq_id_type member data.

TChunks & SetChunks(void)

Assign a value to Chunks data member.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

list< CRef< CID2_Error > > TError

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

void SetGet_data(TGet_data &value)

Assign a value to Get_data data member.

bool IsSetDiscard(void) const

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

bool IsSetBlob_state(void) const

state bits of the blob, 0 or missing means regular live data Check if a value has been assigned to Bl...

TSources & SetSources(void)

Assign a value to Sources data member.

bool IsEmpty(void) const

Check if variant Empty is selected.

bool IsSetVersion(void) const

version of blob, optional in some requests Check if a value has been assigned to Version data member.

const TAnnot_info & GetAnnot_info(void) const

Get the Annot_info member data.

void SetParams(TParams &value)

Assign a value to Params data member.

TBlob_state GetBlob_state(void) const

Get the Blob_state member data.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

const TSeq_id & GetSeq_id(void) const

Get the variant data.

bool IsSetData(void) const

chunk data not set if error occurred Check if a value has been assigned to Data data member.

const TChunk_id & GetChunk_id(void) const

Get the Chunk_id member data.

void SetSat_key(TSat_key value)

Assign a value to Sat_key data member.

TBlob_state GetBlob_state(void) const

Get the Blob_state member data.

list< vector< char > * > TData

TBlob_state GetBlob_state(void) const

Get the Blob_state member data.

const TReply & GetReply(void) const

Get the Reply member data.

E_Choice Which(void) const

Which variant is currently selected.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

TSplit_version GetSplit_version(void) const

Get the Split_version member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

list< CID2S_Chunk_Id > TChunks

CID2_Request_Get_Seq_id TGet_seq_id

Tdata & Set(void)

Assign a value to data member.

TSub_sat GetSub_sat(void) const

Get the Sub_sat member data.

TSerial_number GetSerial_number(void) const

Get the Serial_number member data.

bool IsSetEnd_of_reply(void) const

this Seq-id is the last one in the request Check if a value has been assigned to End_of_reply data me...

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CID2_Request > > Tdata

bool IsSetSerial_number(void) const

request's serial number, copy from request Check if a value has been assigned to Serial_number data m...

bool IsSetError(void) const

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

void SetSat(TSat value)

Assign a value to Sat data member.

const TRequest & GetRequest(void) const

Get the Request member data.

const TData & GetData(void) const

Get the Data member data.

bool IsInit(void) const

Check if variant Init is selected.

void SetRequest(TRequest &value)

Assign a value to Request data member.

bool IsSetData(void) const

blob split info not set if error occurred Check if a value has been assigned to Data data member.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

TSat GetSat(void) const

Get the Sat member data.

void SetSub_sat(TSub_sat value)

Assign a value to Sub_sat data member.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

list< CRef< CSeq_id > > TSeq_id

bool IsSetEnd_of_reply(void) const

true if this reply is the last one for the request false if more replies will follow Check if a value...

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

void SetExternal(void)

Set NULL data member (assign 'NULL' value to External data member).

TSplit_version GetSplit_version(void) const

Get the Split_version member data.

bool IsSetData(void) const

whole blob or blob skeleton not set if error occurred Check if a value has been assigned to Data data...

const TData & GetData(void) const

Get the Data member data.

const Tdata & Get(void) const

Get the member data.

@ eSeq_id_type_hash

return a sequence hash as integer in general id with db "HASH"

@ eSeq_id_type_any

return any qualified Seq-id

@ eSeq_id_type_taxid

return a sequence taxonomy ID as integer in general id with db "TAXID"

@ eSeq_id_type_seq_length

return a sequence Seq-inst.length as int in general id with db "Seq-inst.length"

@ eSeq_id_type_seq_mol

return a sequence Seq-inst.mol as int in general id with db "Seq-inst.mol"

@ eSeq_id_type_text

text Seq-id (accession etc) is preferred

@ eSeq_id_type_gi

gi is preferred

@ eSeq_id_type_label

return a sequence string label as string in general id with db "LABEL"

@ eSeq_id_type_all

return all qualified Seq-ids of the sequence

@ eSeverity_no_data

resolve request gives no data probably temporarily (see retry-delay field)

@ eSeverity_restricted_data

data exists but client doesn't have permission to get it

@ eSeverity_failed_command

command cannot be completed this time

@ eSeverity_failed_server

server cannot be used for a while

@ eSeverity_warning

nothing harmful happened

@ eSeverity_unsupported_command

this request type is not supported by server

@ eSeverity_invalid_arguments

error in request packet, cannot retry

@ eSeverity_failed_connection

connection cannot be reused, reconnect is required

@ eID2_Blob_State_suppressed

@ eID2_Blob_State_protected

@ eID2_Blob_State_suppressed_temp

@ eID2_Blob_State_withdrawn

bool IsSetSeq_loc(void) const

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

bool IsSetName(void) const

name is set if this is named annot name may be empty which differ from unnamed annot Check if a value...

bool IsSetGraph(void) const

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

bool IsSetAlign(void) const

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

const TName & GetName(void) const

Get the Name member data.

bool IsSetFeat(void) const

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

void ResetGraph(void)

Reset Graph data member.

bool IsGeneral(void) const

Check if variant General is selected.

E_Choice Which(void) const

Which variant is currently selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ e_not_set

No variant selected.

EMol

molecule class in living organism

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

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

Static variables safety - create on demand, destroy on application termination.

Multi-threading – mutexes; rw-locks; semaphore.

Helper classes and templates to implement plugins.

#define DEFAULT_DEBUG_LEVEL

static const char kSpecialId_type[]

static void LoadedChunksPacket(CReaderRequestResult &result, CID2_Request_Packet &packet, vector< TChunkId > &chunks, const CBlob_id &blob_id)

NCBI_PARAM_ENUM_DEF_EX(objects::CSeq_id::ESNPScaleLimit, GENBANK, ID2SNP_SCALE_LIMIT, objects::CSeq_id::eSNPScaleLimit_Default, eParam_NoThread, GENBANK_ID2SNP_SCALE_LIMIT)

static const char kSpecialId_taxid[]

#define x_GetReaderName(conn)

static size_t GetMaxIdsRequestSize(void)

static size_t GetMaxChunksRequestSize(void)

typedef NCBI_PARAM_TYPE(GENBANK, ID2SNP_SCALE_LIMIT) TID2SNP_Scale_Limit

static const char kSpecialId_length[]

static const char kSpecialId_label[]

NCBI_PARAM_DECL(int, GENBANK, ID2_DEBUG)

static bool sx_IsSpecialId(const CSeq_id &id)

static bool LimitChunksRequests(size_t max_request_size=GetMaxChunksRequestSize())

NCBI_PARAM_ENUM_DECL(objects::CSeq_id::ESNPScaleLimit, GENBANK, ID2SNP_SCALE_LIMIT)

NCBI_DEFINE_ERR_SUBCODE_X(17)

NCBI_PARAM_ENUM_ARRAY(objects::CSeq_id::ESNPScaleLimit, GENBANK, ID2SNP_SCALE_LIMIT)

static bool SeparateChunksRequests(size_t max_request_size=GetMaxChunksRequestSize())

static const char kSpecialId_hash[]

NCBI_PARAM_DEF_EX(int, GENBANK, ID2_DEBUG, CId2ReaderBase::eTraceError, eParam_NoThread, GENBANK_ID2_DEBUG)

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

Defines CRequestContext class for NCBI C++ diagnostic API.

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

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

CId2ReaderBase::TContentsMask m_ContentMask

list< CRef< CID2S_Seq_annot_Info > > TAnnotInfo

map< CSeq_id_Handle, TSeq_idsInfo > TSeq_idSeq_idsSet

pair< int, CReader::TSeqIds > TSeq_idsInfo

map< CBlob_id, CConstRef< CID2_Reply_Data > > TSkeletons

TSeq_idSeq_idsSet m_Seq_ids

map< string, TSeq_idsInfo > TStringSeq_idsSet

pair< int, TBlob_ids > TBlob_idsInfo

map< CSeq_id_Handle, TBlob_idsInfo > TBlob_idSet

map< CBlob_id, SId2BlobInfo > TBlob_ids

map< CBlob_id, int > TBlobStates

vector< const CID2_Request * > requests

CReader::TConn GetConn() const

vector< SId2ProcessorStage > stages

unique_ptr< CReaderAllocatedConnection > conn

CRef< CID2ProcessorPacketContext > packet_context

CID2Processor::TReplies replies

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