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NCBI C++ ToolKit: src/sra/data_loaders/snp/id2snp_impl.cpp Source File

<

Cont>

Cont::value_type::TObjectType&

(Cont& cont)

obj.

().SetStr(

);

obj.

(

, zoom_level);

hash_pos = acc_filter.

(

);

( hash_pos ==

) {

acc[0] !=

|| acc[1] !=

|| acc[2+

] !=

) {

filter_index = NStr::StringToNumeric<size_t>(filter,

<<m); \

*

=

*

(

);

+= (*it)->size();

: m_CompressData(eCompressData_never),

m_ExplicitBlobState(

),

& driver_name)

unique_ptr<CConfig::TParamTree> app_params;

params = app_params.get();

conf.

(driver_name,

conf.

(driver_name,

( *it2 ==

) {

.m_ExplicitBlobState =

;

( *it2 ==

) {

<<na<<

<<exc);

<<na<<

<<exc);

( exception& exc ) {

<<na<<

<<exc.what());

& acc_ver)

( !acc_ver.empty() ) {

(

* text_id =

.GetTextseq_Id() ) {

( text_id->IsSetAccession() && !text_id->GetAccession().empty() &&

text_id->IsSetVersion() && text_id->GetVersion() > 0 ) {

.m_OriginalSeqIdType = request_type;

->m_SNPTracks.push_back(track);

<

Values>

<

TValues>

dst_ind = pos_index / bit_values;

(

first_offset = pos_index % bit_values ) {

first_count = bit_values - first_offset;

( !bits[dst_ind] ) {

src_ind += first_count;

( src_ind < values.

() ) {

( !bits[dst_ind] ) {

src_ind += bit_values;

skeleton.

().push_back(annot);

( !

(feat_chunks,

*feat_per_graph, feat_per_graph) ) {

chunk.

().Set(chunk_id);

annot_info.

(graph_name);

( !feat_chunks[

] ) {

chunk.

().Set(chunk_id);

Ref<CSerialObject>(split_info);

.SetAnnots().push_back(annot);

.SetAnnots().push_back(annot);

Ref<CSerialObject>(chunk);

.SetMessage(

);

replies.back()->SetEnd_of_reply();

replies.push_back(

(&main_reply));

replies.push_back(

(&main_reply));

annot_info.

().SetWhole_seq_id(*seq_id);

annot_info.

().SetWhole_seq_id(*seq_id);

annot_info.

().SetWhole_seq_id(*seq_id);

replies.back()->SetReply().SetGet_blob_id().SetEnd_of_reply();

replies.back()->SetEnd_of_reply();

( (*it)->GetRequest().IsInit() ) {

( !

->m_Context.m_AllowVDB ) {

( !(*it)->IsSetSerial_number() ) {

( (*it)->GetRequest().Which() ) {

(*it)->SetRequest().SetGet_blob_id());

(*it)->SetRequest().SetGet_blob_info());

(*it)->SetRequest().SetGet_chunks());

packet.

().erase(it);

( ret->m_SNPRequests.empty() ) {

it->second, reply.

().SetGet_seq_id());

it->second, reply.

().SetGet_blob_id());

replies.push_back(

(&reply));

replies.push_back(

(&reply));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

ECompressData m_CompressData

TSNPRequests m_SNPRequests

CRef< CSerialObject > x_LoadBlob(CID2SNPContext &context, SSNPEntryInfo &info)

static bool x_GetAccVer(string &acc_ver, const CSeq_id &id)

static void x_AddSeqIdRequest(CID2_Request_Get_Seq_id &request, CID2SNPProcessorPacketContext::SRequestInfo &info)

CID2_Blob_Id & x_GetBlobId(SSNPEntryInfo &id)

CRef< CID2SNPProcessorContext > CreateContext(void)

void ProcessReply(CID2_Reply &reply, CID2SNPProcessorParams &params, CID2SNPProcessorState &state, TReplies &replies)

void x_ProcessReplyGetBlobId(CID2SNPContext &context, CID2SNPProcessorPacketContext &packet_context, CID2_Reply &main_reply, TReplies &replies, CID2SNPProcessorPacketContext::SRequestInfo &info, CID2_Reply_Get_Blob_Id &reply)

void WriteData(CID2SNPContext &context, const SSNPEntryInfo &seq, CID2_Reply_Data &data, const CSerialObject &obj)

CRef< CID2SNPProcessorState > ProcessPacket(CID2_Request_Packet &packet, CID2SNPProcessorParams &params, TReplies &replies)

bool WorthCompressing(const SSNPEntryInfo &seq)

EProcessStatus x_ProcessGetChunks(CID2SNPContext &context, CID2SNPProcessorPacketContext &packet_context, TReplies &replies, CID2_Request &main_request, CID2S_Request_Get_Chunks &request)

CID2SNPContext m_InitialContext

SSNPEntryInfo x_ResolveBlobId(const CID2_Blob_Id &id)

vector< CRef< CID2_Reply > > TReplies

const CID2SNPContext & GetInitialContext(void) const

CRef< CSerialObject > x_LoadChunk(CID2SNPContext &context, SSNPEntryInfo &entry, int chunk_id)

CSNPDbSeqIterator & GetSeqIterator(SSNPEntryInfo &seq)

EProcessStatus x_ProcessGetBlobId(CID2SNPContext &context, CID2SNPProcessorPacketContext &packet_context, TReplies &replies, CID2_Request &main_request, CID2_Request_Get_Blob_Id &request)

void InitContext(CID2SNPContext &context, const CID2_Request &main_request)

CSNPDb GetSNPDb(const string &na)

~CID2SNPProcessor_Impl(void)

EProcessStatus x_ProcessGetBlobInfo(CID2SNPContext &context, CID2SNPProcessorPacketContext &packet_context, TReplies &replies, CID2_Request &main_request, CID2_Request_Get_Blob_Info &request)

void x_ProcessReplyGetSeqId(CID2SNPContext &context, CID2SNPProcessorPacketContext &packet_context, CID2_Reply &main_reply, TReplies &replies, CID2SNPProcessorPacketContext::SRequestInfo &info, CID2_Reply_Get_Seq_id &reply)

void ResetIteratorCache(SSNPEntryInfo &seq)

CID2SNPProcessor_Impl(const CConfig::TParamTree *params=0, const string &driver_name=kEmptyStr)

CID2S_Feat_type_Info –.

CID2S_Reply_Get_Chunk –.

CID2S_Request_Get_Chunks –.

CID2S_Seq_annot_Info –.

CID2S_Seq_id_Interval –.

CID2_Reply_Get_Blob_Id –.

CID2_Reply_Get_Seq_id –.

CID2_Request_Get_Blob_Id –.

CID2_Request_Get_Blob_Info –.

CID2_Request_Get_Seq_id –.

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.

CObjectOStreamAsnBinary –.

CRef< CSeq_annot > GetOverviewAnnot(CRange< TSeqPos > range, const string &annot_name, TFlags flags=fDefaultFlags) const

CRef< CSeq_id > GetSeqId(void) const

TSeqPos GetCoverageZoom(void) const

TSeqPos GetOverviewZoom(void) const

TSeqPos GetMaxSNPLength(void) const

CRef< CSeq_annot > GetCoverageAnnot(CRange< TSeqPos > range, const string &annot_name, TFlags flags=fDefaultFlags) const

void SetTrack(const CSNPDbTrackIterator &track)

TAnnotSet GetTableFeatAnnots(CRange< TSeqPos > range, const string &annot_name, const SFilter &filter, TFlags flags=fDefaultFlags) const

CRange< TSeqPos > GetSNPRange(void) const

size_t GetVDBSeqIndex(void) const

size_t GetTrackCount() const

TSeqPos GetLength(void) const

Base class for all serializable objects.

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

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

definition of a Culling tree

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

Writer-based output stream.

CZipStreamCompressor – zlib based compression stream processor.

A very basic data-write interface.

const_iterator end() const

const_iterator find(const key_type &key) const

Abstract reader-writer interface classes.

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

main entry point for tests

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

static CNcbiApplicationGuard InstanceGuard(void)

Singleton method.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

@ eNoOwnership

No ownership is assumed.

iterator find(const key_type &key)

void set_size_limit(size_t size_limit)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

#define MSerial_AsnText

I/O stream manipulators –.

static TParamTree * ConvertRegToTree(const IRegistry &reg, NStr::ECase use_case=NStr::eNocase)

Reconstruct param tree from the application registry.

int GetInt(const string &driver_name, const string &param_name, EErrAction on_error, int default_value, const list< string > *synonyms=NULL)

Utility function to get an integer element of parameter tree Throws an exception when mandatory param...

@ eErr_NoThrow

Return default value on error.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string CombineWithZoomLevel(const string &acc, int zoom_level)

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

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

#define NCBI_PARAM_TYPE(section, name)

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

@ eParam_NoThread

Do not use per-thread values.

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

ERW_Result

Result codes for I/O operations.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

@ eRW_Success

Everything is okay, I/O completed.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

CTempString substr(size_type pos) const

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

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.

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

Find the first instance of the entire matching string within the current string, beginning at an opti...

size_type size(void) const

Return the length of the represented array.

@ fConvErr_NoThrow

Do not throw an exception on error.

const TTreeType * FindSubNode(const TKeyType &key) const

Non recursive linear scan of all subnodes, with key comparison.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

void SetType(TType &value)

Assign a value to Type data member.

bool IsSetAnnot_info(void) const

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

bool IsSetValue(void) const

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

const TSources & GetSources(void) const

Get the Sources member data.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

const TChunks & GetChunks(void) const

Get the Chunks member data.

void ResetEnd_of_reply(void)

Reset End_of_reply data member.

void SetSerial_number(TSerial_number value)

Assign a value to Serial_number data member.

bool IsSetEnd_of_reply(void) const

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

void SetSeq_id_type(TSeq_id_type value)

Assign a value to Seq_id_type data member.

TSerial_number GetSerial_number(void) const

Get the Serial_number member data.

TSeq_id_type GetSeq_id_type(void) const

Get the Seq_id_type member data.

bool IsGet_seq_id(void) const

Check if variant Get_seq_id is selected.

TError & SetError(void)

Assign a value to Error data member.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

void SetData(TData &value)

Assign a value to Data data member.

void SetReply(TReply &value)

Assign a value to Reply data member.

list< CRef< CID2_Param > > Tdata

TSources & SetSources(void)

Assign a value to Sources data member.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

const TSeq_id & GetSeq_id(void) const

Get the variant data.

const TBlob_id & GetBlob_id(void) const

Get the variant data.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

list< vector< char > * > TData

const TReply & GetReply(void) const

Get the Reply member data.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

list< CID2S_Chunk_Id > TChunks

bool IsSetSerial_number(void) const

request's serial number, can be used in asynchronic clients server should copy it to corresponding fi...

Tdata & Set(void)

Assign a value to data member.

void ResetEnd_of_reply(void)

Reset End_of_reply data member.

TSerial_number GetSerial_number(void) const

Get the Serial_number member data.

void SetEnd_of_reply(void)

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

const Tdata & Get(void) const

Get the member data.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

void ResetSources(void)

Reset Sources data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetSeq_id(void) const

resolved Seq-id not set if error occurred Check if a value has been assigned to Seq_id data member.

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 IsSetParams(void) const

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

bool IsBlob_id(void) const

Check if variant Blob_id is selected.

const TValue & GetValue(void) const

Get the Value member data.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

TAnnot_info & SetAnnot_info(void)

Assign a value to Annot_info data member.

void SetBlob_id(TBlob_id &value)

Assign a value to Blob_id data member.

bool IsGet_blob_id(void) const

Check if variant Get_blob_id is selected.

const TParams & GetParams(void) const

Get the Params member data.

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 SetChunk_id(const TChunk_id &value)

Assign a value to Chunk_id data member.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSeq_id(void) const

Check if variant Seq_id is selected.

bool IsSetBlob_id(void) const

result Check if a value has been assigned to Blob_id data member.

bool IsSetSources(void) const

return id of blob with sequence Check if a value has been assigned to Sources data member.

@ eData_type_id2s_split_info

@ eSeq_id_type_any

return any qualified Seq-id

@ eSeq_id_type_text

text Seq-id (accession etc) is preferred

@ 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)

@ eData_format_asn_binary

void SetName(const TName &value)

Assign a value to Name data member.

void SetType(TType value)

Assign a value to Type data member.

TSubtypes & SetSubtypes(void)

Assign a value to Subtypes data member.

void SetSkeleton(TSkeleton &value)

Assign a value to Skeleton data member.

void SetId(const TId &value)

Assign a value to Id data member.

void SetSeq_loc(TSeq_loc &value)

Assign a value to Seq_loc data member.

TChunks & SetChunks(void)

Assign a value to Chunks data member.

void SetStart(TStart value)

Assign a value to Start data member.

TData & SetData(void)

Assign a value to Data data member.

TFeat & SetFeat(void)

Assign a value to Feat data member.

TContent & SetContent(void)

Assign a value to Content data member.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

void SetGraph(void)

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

void SetLength(TLength value)

Assign a value to Length data member.

TFrom GetFrom(void) const

Get the From member data.

const TInt & GetInt(void) const

Get the variant data.

const TInt & GetInt(void) const

Get the variant data.

const TGraph & GetGraph(void) const

Get the Graph member data.

const TValues & GetValues(void) const

Get the Values member data.

const TByte & GetByte(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

bool IsByte(void) const

Check if variant Byte is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

TNumval GetNumval(void) const

Get the Numval member data.

TComp GetComp(void) const

Get the Comp member data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

void SetId(TId &value)

Assign a value to Id data member.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TGraph & GetGraph(void) const

Get the variant data.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

const TData & GetData(void) const

Get the Data member data.

#define DEFAULT_COMPRESS_DATA

SSNPDbTrackInfo ParseTrack(CTempString acc_filter)

static const TSeqPos kGraphChunkSize

static const EResolveMaster kResolveMaster

bool sx_HasNonZero(const Values &values, TSeqPos index, TSeqPos count)

#define DEFAULT_VDB_CACHE_SIZE

static bool s_FilterAll(void)

const int kFilterIndexCount

const int kNAVersionDigitsMin

static bool s_Enabled(void)

void sx_SetZoomLevel(CSeq_annot &annot, int zoom_level)

string FormatTrack(const SSNPDbTrackInfo &track)

static const TSeqPos kFeatChunkSize

const int kNAVersionDigitsMax

static void sx_AddBits(vector< char > &bits, TSeqPos kChunkSize, const CSeq_graph &graph)

static int s_DebugLevel(void)

const int kFilterIndexMaxLength

bool IsValidFilterIndex(size_t filter_index)

static const int kChunkIdMul

CNcbiOstream & operator<<(CNcbiOstream &out, const CID2SNPProcessor_Impl::SSNPEntryInfo &seq)

static bool s_DebugEnabled(EDebugLevel level)

bool IsValidNAVersion(size_t na_version)

NCBI_PARAM_DEF_EX(bool, ID2SNP, ENABLE, true, eParam_NoThread, ID2SNP_ENABLE)

static const int kChunkIdFeat

static const int kChunkIdGraph

@ eResolveMaster_without_gi

bool IsValidSeqIndex(size_t seq_index)

NCBI_DEFINE_ERR_SUBCODE_X(24)

bool IsValidNAIndex(size_t na_index)

string GetNAAccession(const SSNPDbTrackInfo &track)

void sx_AddBits2(vector< char > &bits, TSeqPos bit_values, TSeqPos pos_index, const TValues &values)

size_t sx_GetSize(const CID2_Reply_Data &data)

Cont::value_type::TObjectType & sx_AddNew(Cont &cont)

NCBI_PARAM_DECL(bool, ID2SNP, ENABLE)

#define NCBI_ID2PROC_SNP_PARAM_COMPRESS_DATA

#define NCBI_ID2PROC_SNP_PARAM_VDB_CACHE_SIZE

Definition of all error codes used in SRA C++ support libraries.

double value_type

The numeric datatype used by the parser.

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

string s_Value(TValue value)

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

Reader-writer based streams.

vector< SSNPDbTrackInfo > m_SNPTracks

CSNPDbSeqIterator m_SeqIter

CRef< CID2_Blob_Id > m_BlobId

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

static CS_CONTEXT * context

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