NCBI C++ ToolKit
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Defines BLAST database access classes. More...
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <objtools/blast/seqdb_reader/seqdbblob.hpp>
#include <objects/blastdb/Blast_def_line.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/blastdb/defline_extra.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/blastdb/Blast_db_metadata.hpp>
#include <objects/blastdb/Blast_db_mask_info.hpp>
#include <util/sequtil/sequtil.hpp>
#include <util/range.hpp>
#include <set>
#include <objmgr/bioseq_handle.hpp>
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Classes | |
class | CSeqDBIter |
CSeqDBIter. More... | |
class | CSeqDB |
CSeqDB. More... | |
struct | CSeqDB::TOffsetPair |
Structure to represent a range. More... | |
struct | CSeqDB::TSequenceRanges |
List of sequence offset ranges. More... | |
struct | SSeqDBInitInfo |
Structure to define basic information to initialize a BLAST DB. More... | |
class | CSeqDBSequence |
CSeqDBSequence –. More... | |
Functions | |
USING_SCOPE (objects) | |
Include definitions from the objects namespace. More... | |
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. More... | |
CSeqDB::ESeqType | ParseMoleculeTypeString (const string &str) |
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... | |
Defines BLAST database access classes.
Defines classes: CSeqDB CSeqDBSequence
Implemented for: UNIX, MS-Windows
Definition in file seqdb.hpp.
bool DeleteBlastDb | ( | const string & | dbpath, |
CSeqDB::ESeqType | seq_type | ||
) |
Deletes all files associated with a BLAST database.
dbpath | BLAST database file path [in] |
seq_type | Sequence type [in] |
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().
vector<SSeqDBInitInfo> FindBlastDBs | ( | const string & | path, |
const string & | dbtype, | ||
bool | recurse, | ||
bool | include_alias_files = false , |
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bool | remove_redundant_dbs = false |
||
) |
Find BLAST DBs in the directory specified.
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().
CSeqDB::ESeqType ParseMoleculeTypeString | ( | const string & | str | ) |
Convert a string to a CSeqDB ESeqType object.
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().
USING_SCOPE | ( | objects | ) |
Include definitions from the objects namespace.