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NCBI C++ ToolKit: src/objtools/data_loaders/blastdb/remote_blastdb_adapter.cpp Source File

use_fixed_size_slices)

: m_DbName(db_name), m_DbType(db_type), m_NextLocalId(1),

m_UseFixedSizeSlices(use_fixed_size_slices)

<< (

?

:

) <<

<<

<< db_name <<

;

[oid].GetLength();

[oid].GetIdList();

retval =

;

(

(errors,

) !=

) {

( !errors.empty() ) {

( !warnings.empty() ) {

+= (

.empty() ? warnings :

+ warnings);

=

;

+=

;

errors, warnings;

kVerbose = (getenv(

) ?

:

);

errors, warnings, kVerbose);

(seq_data.empty() || !errors.empty() || !warnings.empty() ||

(ids.size() == seq_data.size());

vector<TSeqRange>& ranges)

seqids.reserve(oids.size());

(vector<int>::size_type

= 0;

< oids.size();

++) {

ranges[

].GetToOpen()) );

ranges[

].GetFrom(), ranges[

].GetToOpen()));

seqids.push_back(seq_int);

errors, warnings;

kVerbose = (getenv(

) ?

:

);

errors, warnings, kVerbose);

(seq_data.empty() || !errors.empty() || !warnings.empty() ||

(seqids.size() == ids.size());

(ids.size() == seq_data.size());

(vector<int>::size_type

= 0;

< oids.size();

++) {

ranges[

].GetToOpen()) = seq_data[

];

ranges[

].GetToOpen()));

vector<TSeqRange>& ranges,

(oids.size() == ranges.size());

sequence_data.clear();

vector<int> oids2fetch;

vector<TSeqRange> ranges2fetch;

(vector<int>::size_type

= 0;

< oids.size();

++) {

begin = 0, end = cached_seqdata.

();

begin = ranges[

].GetFrom();

end = ranges[

].GetToOpen();

oids2fetch.push_back(oids[

]);

ranges2fetch.push_back(

(begin, end-1));

(ranges[

] == ranges2fetch.back());

sequence_data.reserve(oids.size());

(vector<int>::size_type

= 0;

< oids.size();

++) {

begin = 0, end = cached_seqdata.

();

begin = ranges[

].GetFrom();

end = ranges[

].GetToOpen();

(sequence_data.size() == oids.size());

(vector<int>::size_type

= 0;

< sequence_data.size();

++) {

kVerbose = (getenv(

) ?

:

);

errors, warnings;

warnings, kVerbose,

);

( !errors.empty() || !warnings.empty() || bioseqs.empty() ) {

(bioseqs.size() == seqids.size());

cached_seqdata.

(bioseqs.front()->GetLength(),

cached_seqdata.

(bioseqs.front()->SetId());

cached_seqdata.

(bioseqs.front());

cached_seqdata.

();

oids.reserve(ids.size());

(vector<int>::size_type

= 0;

< ids.size();

++) {

kVerbose = (getenv(

) ?

:

);

errors, warnings;

(

vector< CRef<CSeq_id>

& >(*&ids),

, seqtype,

bioseqs, errors, warnings, kVerbose,

);

( !errors.empty() || !warnings.empty() || bioseqs.empty() ) {

(bioseqs.size() == ids.size());

(vector<int>::size_type

= 0;

< oids.size();

++) {

cached_seqdata.

(bioseqs[

]->SetId());

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.

Declares the CBlastServices class.

API for Remote Blast Services.

This class defines a "bundle" of elements to cache which are then returned by CRemoteBlastDbAdapter.

void SetBioseq(CRef< CBioseq > bioseq)

Set the Bioseq associated with a given sequence.

IBlastDbAdapter::TSeqIdList GetIdList() const

Retrieve the Seq-id's associated with a given sequence.

TSeqPos GetLength() const

Retrieve the sequence length.

bool IsValid()

Returns true if this object has been properly initialized and it's ready to be used.

bool HasSequenceData(int begin, int end)

Returns true if the requested range has sequence data already.

void SetLength(TSeqPos length, bool use_fixed_size_slices)

Sets the length of the sequence data for a given Bioseq.

CRef< CSeq_data > & GetSeqDataChunk(int begin, int end)

Access the sequence data chunk for a given starting and ending offset.

void SetIdList(const IBlastDbAdapter::TSeqIdList &idlist)

Sets the Seq-id's associated with a given sequence param idlist IDs to assign to this object [in].

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

This class allows retrieval of sequence data from BLAST databases at NCBI.

virtual bool SeqidToOid(const CSeq_id &id, int &oid)

@inheritDoc

bool SeqidToOidBatch(const vector< CRef< CSeq_id > > &ids, vector< int > &oids)

Batch-version of SeqidToOid.

virtual CSeqDB::ESeqType GetSequenceType()

@inheritDoc

virtual TSeqIdList GetSeqIDs(int oid)

@inheritDoc

void GetSequenceBatch(const vector< int > &oids, const vector< TSeqRange > &ranges, vector< CRef< CSeq_data > > &sequence_data)

Batch-version of GetSequence.

int m_NextLocalId

Our local "OID generator".

virtual int GetSeqLength(int oid)

@inheritDoc

map< int, CCachedSeqDataForRemote > m_Cache

Internal cache, maps OIDs to CCachedSeqDataForRemote.

virtual CRef< CSeq_data > GetSequence(int oid, int begin=0, int end=0)

@inheritDoc

virtual CRef< CBioseq > GetBioseqNoData(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_id=NULL)

@inheritDoc

string m_DbName

BLAST database name.

void x_FetchData(int oid, int begin, int end)

This method actually retrieves the sequence data.

bool m_UseFixedSizeSlices

Determines whether sequences should be fetched in fixed size slices or in incrementally larger sizes.

void x_FetchDataByBatch(const vector< int > &oids, const vector< TSeqRange > &ranges)

list< CRef< CSeq_id > > TSeqIdList

Convenience typedef for a list of CSeq_id-s.

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

main entry point for tests

static void GetSequenceParts(const TSeqIntervalVector &seqids, const string &database, char seqtype, TSeqIdVector &ids, TSeqDataVector &seq_data, string &errors, string &warnings, bool verbose=false)

This retrieves (partial) sequence data from the remote BLAST server.

static void GetSequencesInfo(TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false)

Get a set of Bioseqs without their sequence data given an input set of.

bool IsValidBlastDb(const string &dbname, bool is_protein)

Returns true if the BLAST database specified exists in the NCBI servers.

vector< CRef< objects::CSeq_data > > TSeqDataVector

Defines a std::vector of CRef<CSeq_data>

vector< CRef< objects::CBioseq > > TBioseqVector

Defines a std::vector of CRef<CBioseq>

vector< CRef< objects::CSeq_interval > > TSeqIntervalVector

Defines a std::vector of CRef<CSeq_interval>

vector< CRef< objects::CSeq_id > > TSeqIdVector

Defines a std::vector of CRef<CSeq_id>

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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)

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

Set object to copy of another one.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

static TThisType GetEmpty(void)

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

static bool RemoteBlastDbLoader_ErrorHandler(const string &errors, const string &warnings)

Returns false always.

Declaration of the CRemoteBlastDbAdapter class.

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

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