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NCBI C++ ToolKit: include/objtools/blast/seqdb_writer/multisource_util.hpp Source File

vector<string> & keys);

eArg:

;

m_GisOids.reserve(capacity);

m_CurrentOrder =

;

(m_CurrentOrder ==

) {

m_CurrentOrder =

;

}

(m_Last == gi) {

m_GisOids.push_back(

(gi, oid));

m_CurrentOrder =

;

(str_id !=

) m_SisOids.push_back(

(str_id, oid));

vector<string> & lines);

: m_SeqDB(seqdb), m_Buffer(

)

m_SeqDB.RetSequence(& m_Buffer);

User-defined methods of the data storage class.

Gi List for database construction.

void AppendSi(const string &si, int oid=-1)

Append a Seq-id.

CInputGiList(int capacity=1024)

Construct an empty GI list.

void AppendGi(TGi gi, int oid=-1)

Append a GI.

@ eArg

Argument validation failed.

virtual const char * GetErrCodeString() const override

Get a message describing the exception.

NCBI_EXCEPTION_DEFAULT(CMultisourceException, CException)

Include standard NCBI exception behavior.

CSequenceReturn(CSeqDB &seqdb, const char *buffer)

CSequenceReturn & operator=(CSequenceReturn &)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char si[8][64]

TErrCode GetErrCode(void) const

Get error code.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_XOBJWRITE_EXPORT

string AccessionToKey(const string &acc)

bool CheckAccession(const string &acc, TGi &gi, CRef< objects::CSeq_id > &seqid, bool &specific)

void GetDeflineKeys(const objects::CBlast_def_line &defline, vector< string > &keys)

Get all keys for a defline.

void MapToLMBits(const TLinkoutMap &gilist, TIdToBits &gi2links)

Read a set of GI lists, each a vector of strings, and combine the bits into the resulting linkbits ma...

map< string, CBlast_def_line::TTaxIds > TIdToLeafs

Map from Seq-id string to set of leaf taxids.

map< string, int > TIdToBits

Maps Seq-id key to bitset.

void ReadTextFile(CNcbiIstream &f, vector< string > &lines)

map< int, vector< string > > TLinkoutMap

Map from linkout bit number to list of ids.

void GetSeqIdKey(const objects::CSeq_id &id, string &key)

const struct ncbi::grid::netcache::search::fields::KEY key

Defines BLAST database access classes.

ESeqDBIdType SeqDB_SimplifyAccession(const string &acc, Int8 &num_id, string &str_id, bool &simpler)

String id simplification.

Structure that holds GI,OID pairs.

Structure that holds Seq-id,OID pairs.

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