seqdb.cpp File Reference

Implementation for the CSeqDB class, the top level class for SeqDB. More...

#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include "seqdbimpl.hpp"
#include <objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp>
#include <map>
#include <string>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/objistrasnb.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Dbtag.hpp>

Include dependency graph for seqdb.cpp:

Go to the source code of this file.

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Classes
class	CBlastDbFinder
	Functor class for FindFilesInDir. More...
class	PathFinder
	Functor object for s_RemoveAliasComponents where the path name is matched in SSeqDBInitInfo. More...

Functions
static char	s_GetSeqTypeChar (CSeqDB::ESeqType seqtype)
	Helper function to translate enumerated type to character. More...
static CSeqDBImpl *	s_SeqDBInit (const string &dbname, char prot_nucl, int oid_begin, int oid_end, bool use_atlas_lock, CSeqDBGiList *gi_list=NULL, CSeqDBNegativeList *neg_list=NULL, CSeqDBIdSet idset=CSeqDBIdSet())
	Helper function to build private implementation object. More...
static void	s_RemoveAliasComponents (CBlastDbFinder &finder)
vector< SSeqDBInitInfo >	FindBlastDBs (const string &path, const string &dbtype, bool recurse, bool include_alias_files, bool remove_redundant_dbs)
	Find BLAST DBs in the directory specified. More...
CSeqDB::ESeqType	ParseMoleculeTypeString (const string &s)
	Convert a string to a CSeqDB ESeqType object. More...
bool	DeleteBlastDb (const string &dbpath, CSeqDB::ESeqType seq_type)
	Deletes all files associated with a BLAST database. More...

Detailed Description

Implementation for the CSeqDB class, the top level class for SeqDB.

Definition in file seqdb.cpp.

Function Documentation

DeleteBlastDb()

bool DeleteBlastDb	(	const string &	dbpath,
		CSeqDB::ESeqType	seq_type
	)

Deletes all files associated with a BLAST database.

Parameters

dbpath	BLAST database file path [in]
seq_type	Sequence type [in]

Returns

true if relevant files were deleted, else false

Definition at line 1542 of file seqdb.cpp.

References eBDB_Version4, CSeqDB::eProtein, f, CSeqDB::FindVolumePaths(), Info(), NStr::IntToString(), ITERATE, LOG_POST, CDirEntry::Remove(), SeqDB_GetFileExtensions(), and SeqDB_GetLMDBFileExtensions().

Referenced by BOOST_AUTO_TEST_CASE(), CBuildDatabase::CBuildDatabase(), CBlastdbConvertApp::Run(), BlastdbCopyApplication::Run(), and s_DeleteMakeprofileDb().

FindBlastDBs()

vector<SSeqDBInitInfo> FindBlastDBs	(	const string &	path,
		const string &	dbtype,
		bool	recurse,
		bool	include_alias_files = false,
		bool	remove_redundant_dbs = false
	)

Find BLAST DBs in the directory specified.

Parameters

path	directory to search BLAST DBs [in]
dbtype	BLAST DB molecule type, allowed values are 'prot', 'nucl', and 'guess' (which means any) [in]
recurse	whether BLAST DBs should be found recursively or not [in]
include_alias_files	Should alias files be included also? [in]
remove_redundant_dbs	Should BLASTDBs that are referenced by other alias files in the return value be removed? [in]

Definition at line 1429 of file seqdb.cpp.

References fFF_File, fFF_Recursive, FindFilesInDir(), flags, CBlastDbFinder::m_DBs, s_RemoveAliasComponents(), and ct::sort().

Referenced by CDirTest::Test().

ParseMoleculeTypeString()

CSeqDB::ESeqType ParseMoleculeTypeString

(

const string &

str

)

Convert a string to a CSeqDB ESeqType object.

Parameters

str	string containing the molecule type (e.g.: prot, nucl, guess)

Definition at line 1527 of file seqdb.cpp.

References _ASSERT, NStr::eNocase, CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::eUnknown, and NStr::StartsWith().

Referenced by CBuildDatabase::CBuildDatabase(), CBlastdbConvertApp::Run(), BlastdbCopyApplication::Run(), CDbTest::Test(), CBlastDBCmdApp::x_InitBlastDB(), and CBlastDBCmdApp::x_InitBlastDB_TaxIdList().

s_GetSeqTypeChar()

static char s_GetSeqTypeChar ( CSeqDB::ESeqType  seqtype )

static

Helper function to translate enumerated type to character.

Parameters

seqtype

The sequence type (eProtein, eNucleotide, or eUnknown).

Returns

The sequence type as a char ('p', 'n', or '-').

Definition at line 62 of file seqdb.cpp.

References CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::eUnknown, and NCBI_THROW.

Referenced by CSeqDB::CSeqDB().

s_RemoveAliasComponents()

static void s_RemoveAliasComponents ( CBlastDbFinder &  finder )

static

Definition at line 1397 of file seqdb.cpp.

References NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, CBlastDbFinder::GetFileName(), i, in(), set< Key, Compare >::insert(), ITERATE, CBlastDbFinder::m_DBs, remove_if(), NStr::Split(), and NStr::StartsWith().

Referenced by FindBlastDBs().

s_SeqDBInit()

static CSeqDBImpl* s_SeqDBInit ( const string &  dbname, char  prot_nucl, int  oid_begin, int  oid_end, bool  use_atlas_lock, CSeqDBGiList *  gi_list = NULL, CSeqDBNegativeList *  neg_list = NULL, CSeqDBIdSet  idset = CSeqDBIdSet()  )

static

Helper function to build private implementation object.

This method builds and returns the object which implements the functionality for the CSeqDB API. If this method is called with '-' for the sequence data type, protein will be tried first, then nucleotide. The created object will be returned. Either kSeqTypeProt for a protein database, kSeqTypeNucl for nucleotide, or kSeqTypeUnkn to less this function try one then the other.

Parameters

dbname	A list of database or alias names, seperated by spaces.
prot_nucl	Specify whether to use protein, nucleotide, or either.
oid_begin	Iterator will skip OIDs less than this value. Only OIDs found in the OID lists (if any) will be returned.
oid_end	Iterator will return up to (but not including) this OID.
use_mmap	If kSeqDBMMap is specified (the default), memory mapping is attempted. If kSeqDBNoMMap is specified, or memory mapping fails, this platform does not support it, the less efficient read and write calls are used instead.
gi_list	This ID list specifies OIDs and deflines to include.
neg_list	This negative ID list specifies deflines and OIDs to exclude.
idset	If set, this specifies IDs to either include or exclude.

Returns

The CSeqDBImpl object that was created.

Definition at line 111 of file seqdb.cpp.

References _ASSERT, and dbname().

Referenced by CSeqDB::CSeqDB().