NCBI C++ ToolKit
Classes | Typedefs | Functions
multisource_util.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/blastdb/Blast_def_line.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
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Classes

class  CMultisourceException
 CMultisourceException. More...
 
class  CInputGiList
 Gi List for database construction. More...
 
class  CSequenceReturn
 

Typedefs

typedef map< string, intTIdToBits
 Maps Seq-id key to bitset. More...
 
typedef map< string, CBlast_def_line::TTaxIdsTIdToLeafs
 Map from Seq-id string to set of leaf taxids. More...
 
typedef map< int, vector< string > > TLinkoutMap
 Map from linkout bit number to list of ids. More...
 

Functions

void GetDeflineKeys (const objects::CBlast_def_line &defline, vector< string > &keys)
 Get all keys for a defline. More...
 
void ReadTextFile (CNcbiIstream &f, vector< string > &lines)
 
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 map. More...
 
bool CheckAccession (const string &acc, TGi &gi, CRef< objects::CSeq_id > &seqid, bool &specific)
 
void GetSeqIdKey (const objects::CSeq_id &id, string &key)
 
string AccessionToKey (const string &acc)
 

Typedef Documentation

◆ TIdToBits

typedef map<string, int> TIdToBits

Maps Seq-id key to bitset.

Definition at line 165 of file multisource_util.hpp.

◆ TIdToLeafs

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

Definition at line 168 of file multisource_util.hpp.

◆ TLinkoutMap

typedef map<int, vector<string> > TLinkoutMap

Map from linkout bit number to list of ids.

Definition at line 171 of file multisource_util.hpp.

Function Documentation

◆ AccessionToKey()

string AccessionToKey ( const string acc)

◆ CheckAccession()

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

◆ GetDeflineKeys()

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

Get all keys for a defline.

Definition at line 162 of file multisource_util.cpp.

References GetSeqIdKey(), ITERATE, and ncbi::grid::netcache::search::fields::key.

Referenced by CTaxIdSet::x_SelectBestTaxid(), and CBuildDatabase::x_SetLinkAndMbit().

◆ GetSeqIdKey()

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

◆ MapToLMBits()

void MapToLMBits ( const TLinkoutMap gilist,
TIdToBits id2links 
)

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

Definition at line 66 of file multisource_util.cpp.

References AccessionToKey(), ITERATE, and ncbi::grid::netcache::search::fields::key.

Referenced by CBuildDatabase::SetLinkouts(), and CBuildDatabase::SetMembBits().

◆ ReadTextFile()

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

Definition at line 43 of file multisource_util.cpp.

References f(), and NcbiGetlineEOL().

Modified on Sun Apr 14 05:24:22 2024 by modify_doxy.py rev. 669887