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

vector<SBlastDbMaskData> & mask_ranges,

vector<int> & column_ids,

vector<CTempString> & column_blobs) = 0;

& title,

long_seqids =

,

limit_defline =

,

scan_bioseq_4_cfastareader_usrobj =

);

& title,

long_seqids =

,

limit_defline =

,

scan_bioseq_4_cfastareader_usrobj =

);

SetMaskLetters(

& mask_letters);

SetSourceDb(

& src_db_name);

Build(

vector<string> & ids,

AddIds(

vector<string> & ids);

AddSequences(

& src,

add_pig =

);

EndBuild(

erase =

);

m_UseRemote = use_remote;

m_SkipCopyingGis = v;

SetMaxFileSize(

max_file_size);

& options,

& name =

);

RegisterMaskingAlgorithm(

& program,

& description,

& options);

CreateDirectories(

&

);

objects::CScope & x_GetScope();

objects::CSeqVector * sv,

add_pig =

);

x_ReportUnresolvedIds(

& gi_list)

;

x_AddOneRemoteSequence(

objects::CSeq_id & seqid,

x_EndBuild(

erase,

* close_exception);

Build BlastDB format databases from various data sources.

bool m_IsProtein

True for a protein database, false for nucleotide.

int m_DeflineCount

Define count.

void x_SetLeafTaxids(CRef< objects::CBlast_def_line_set > headers)

Store leaf taxids in provided headers.

bool m_KeepLinks

True to keep linkout bits from source dbs, false to discard.

bool m_SkipLargeGis

If set to true, skip GIs with value > 0x7FFFFFFF.

TIdToBits m_Id2Links

Table of linkout bits to apply to sequences.

bool m_FoundMatchingMasks

If true, there were sequences whose IDs matched those in the provided masking locations (via SetMaskD...

void SetVerbosity(bool v)

Specify level of output verbosity.

bool m_UseRemote

Whether to use remote resolution and sequence fetching.

bool m_ParseIDs

If true, string IDs found in FASTA input will be parsed as Seq-ids.

int m_OIDCount

Number of OIDs stored in this database.

void SetUseRemote(bool use_remote)

Specify whether to use remote fetching for locally absent IDs.

bool m_ScanBioseq4CFastaReaderUsrObjct

bool m_KeepMbits

True to keep membership bits from source dbs, false to discard.

CRef< CTaxIdSet > m_Taxids

Set of TaxIDs configured to apply to sequences.

CRef< objects::CScope > m_Scope

Sequence scope, used for remote fetching.

CRef< objects::CObjectManager > m_ObjMgr

Object manager, used for remote fetching.

ostream & m_LogFile

Logfile.

bool m_Verbose

If true, more detailed log messages will be produced.

bool m_KeepLeafs

True to keep leaf taxids from source dbs, false to discard.

bool m_SkipCopyingGis

If set to true, when copying BLASTDBs, skip the GIs.

CRef< CWriteDB > m_OutputDb

Database being produced here.

CRef< CSeqDBExpert > m_SourceDb

Database for duplicating sequences locally (-sourcedb option.)

CRef< IMaskDataSource > m_MaskData

Subject masking data.

bool m_LongIDs

If true, use long sequence ids (database|accession)

TIdToLeafs m_Id2Leafs

Table of leaf taxids to apply to sequences.

string GetOutputDbName() const

TIdToBits m_Id2Mbits

Table of membership bits to apply to sequences.

void SetSkipCopyingGis(bool v)

Gi List for database construction.

This represents a set of masks for a given sequence.

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

int TIndexType

Bitwise OR of "EIndexType".

Interface to a source of Bioseq objects.

virtual CConstRef< objects::CBioseq > GetNext()=0

Get a Bioseq object if there are any more to get.

An interface providing lookups of mask-data by Seq-id.

virtual CMaskedRangesVector & GetRanges(const list< CRef< CSeq_id > > &id)=0

Get ranges of masking data for the given Seq-ids.

Interface to a source of raw sequence data.

virtual const map< string, string > & GetColumnMetaData(int id)=0

Get metadata for the column with the specified Column ID.

virtual bool GetNext(CTempString &sequence, CTempString &ambiguities, CRef< objects::CBlast_def_line_set > &deflines, vector< SBlastDbMaskData > &mask_ranges, vector< int > &column_ids, vector< CTempString > &column_blobs)=0

Get a raw sequence.

virtual void GetColumnNames(vector< string > &names)=0

Get the names of all columns defined by this sequence source.

virtual int GetColumnId(const string &name)=0

Get the column ID for a column mentioned by name.

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

static const struct name_t names[]

uint64_t Uint8

8-byte (64-bit) unsigned integer

#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

EBlast_filter_program

This defines the possible sequence filtering algorithms to be used in a BLAST database.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

EBlastDbVersion

BLAST database version.

Defines `expert' version of CSeqDB interfaces.

Class which defines sequence id to taxid mapping.

Defines BLAST database construction classes.

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