#include <objtools/blast/seqdb_reader/seqdbexpert.hpp>

Inheritance diagram for CSeqDBExpert:

Collaboration diagram for CSeqDBExpert:

Public Member Functions
	CSeqDBExpert (const string &dbname, ESeqType seqtype, CSeqDBGiList *gilist=0)
	Short Constructor. More...

	CSeqDBExpert (const string &dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList *gi_list=0)
	Constructor with MMap Flag and OID Range. More...

	CSeqDBExpert ()
	Null Constructor. More...

	~CSeqDBExpert ()
	Destructor. More...

void	GetRawSeqAndAmbig (int oid, const char *buffer, int seq_length, int *ambig_length) const
	Raw Sequence and Ambiguity Data. More...

void	GetGiBounds (TGi low_id, TGi high_id, int *count)
	Get GI Bounds. More...

void	GetPigBounds (int low_id, int high_id, int *count)
	Get PIG Bounds. More...

void	GetStringBounds (string low_id, string high_id, int *count)
	Get String Bounds. More...

unsigned	GetSequenceHash (int oid)
	Get the sequence hash for a given OID. More...

void	HashToOids (unsigned hash, vector< int > &oids)
	Get the OIDs for a given sequence hash. More...

void	Verify ()
	Verify internal SeqDB data structures for consistency. More...

Public Member Functions inherited from CSeqDB
	CSeqDB (const string &dbname, ESeqType seqtype, CSeqDBGiList *gilist=0, bool use_atlas_lock=true)
	Short Constructor. More...

	CSeqDB (const string &dbname, ESeqType seqtype, CSeqDBNegativeList *nlist)
	Short Constructor with Negative ID list. More...

	CSeqDB (const string &dbname, ESeqType seqtype, CSeqDBGiList gilist, CSeqDBNegativeList nlist)
	Short Constructor with Positive and Negative ID list. More...

	CSeqDB (const string &dbname, ESeqType seqtype, int oid_begin, int oid_end, CSeqDBGiList gilist, CSeqDBNegativeList nlist)
	Short Constructor with Positive and Negative ID list with oid range. More...

	CSeqDB (const string &dbname, ESeqType seqtype, CSeqDBIdSet ids)
	Short Constructor with Computed ID list. More...

	CSeqDB (const vector< string > &dbs, ESeqType seqtype, CSeqDBGiList *gilist=0)
	Short Constructor. More...

	CSeqDB (const string &dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList *gi_list=0)
	Constructor with MMap Flag and OID Range. More...

	CSeqDB (const vector< string > &dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList *gi_list=0)
	Constructor with MMap Flag and OID Range. More...

	~CSeqDB ()
	Destructor. More...

int	GetSeqLength (int oid) const
	Returns the sequence length in base pairs or residues. More...

TGi	GetSeqGI (int oid) const
	Returns the first Gi (if any) of the sequence. More...

int	GetSeqLengthApprox (int oid) const
	Returns an unbiased, approximate sequence length. More...

CRef< CBlast_def_line_set >	GetHdr (int oid) const
	Get the ASN.1 header for the sequence. More...

void	GetLeafTaxIDs (int oid, map< TGi, set< TTaxId > > &gi_to_taxid_set, bool persist=false) const
	Get taxid for an OID. More...

void	GetLeafTaxIDs (int oid, vector< TTaxId > &taxids, bool persist=false) const
	Get taxids for an OID. More...

void	GetTaxIDs (int oid, map< TGi, TTaxId > &gi_to_taxid, bool persist=false) const
	Get taxid for an OID. More...

void	GetTaxIDs (int oid, vector< TTaxId > &taxids, bool persist=false) const
	Get taxids for an OID. More...

void	GetAllTaxIDs (int oid, set< TTaxId > &taxids) const
	Get all tax ids for an oid. More...

CRef< CBioseq >	GetBioseq (int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const
	Get a CBioseq for a sequence. More...

CRef< CBioseq >	GetBioseqNoData (int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const
	Get a CBioseq for a sequence without sequence data. More...

int	GetSequence (int oid, const char **buffer) const
	Get a pointer to raw sequence data. More...

int	GetAmbigSeq (int oid, const char **buffer, int nucl_code) const
	Get a pointer to sequence data with ambiguities. More...

int	GetAmbigSeq (int oid, const char **buffer, int nucl_code, int begin_offset, int end_offset) const
	Get a pointer to a range of sequence data with ambiguities. More...

int	GetAmbigSeqAlloc (int oid, char *buffer, int nucl_code, ESeqDBAllocType strategy, TSequenceRanges masks=NULL) const
	Get a pointer to sequence data with ambiguities. More...

int	GetAmbigPartialSeq (int oid, char *buffer, int nucl_code, ESeqDBAllocType strategy, TSequenceRanges partial_ranges, TSequenceRanges *masks=NULL) const

void	RetSequence (const char **buffer) const
	Returns any resources associated with the sequence. More...

void	RetAmbigSeq (const char **buffer) const
	Returns any resources associated with the sequence. More...

list< CRef< CSeq_id > >	GetSeqIDs (int oid) const
	Gets a list of sequence identifiers. More...

void	GetGis (int oid, vector< TGi > &gis, bool append=false) const
	Gets a list of GIs for an OID. More...

ESeqType	GetSequenceType () const
	Returns the type of database opened - protein or nucleotide. More...

string	GetTitle () const
	Returns the database title. More...

string	GetDate () const
	Returns the construction date of the database. More...

int	GetNumSeqs () const
	Returns the number of sequences available. More...

int	GetNumSeqsStats () const
	Returns the number of sequences available. More...

int	GetNumOIDs () const
	Returns the size of the (possibly sparse) OID range. More...

Uint8	GetTotalLength () const
	Returns the sum of the lengths of all available sequences. More...

Uint8	GetExactTotalLength ()
	Returns the exact sum of the lengths of all available sequences. More...

Uint8	GetTotalLengthStats () const
	Returns the sum of the lengths of all available sequences. More...

Uint8	GetVolumeLength () const
	Returns the sum of the lengths of all volumes. More...

void	GetTotals (ESummaryType sumtype, int oid_count, Uint8 total_length, bool use_approx=true) const
	Returns the sum of the sequence lengths. More...

int	GetMaxLength () const
	Returns the length of the largest sequence in the database. More...

int	GetMinLength () const
	Returns the length of the shortest sequence in the database. More...

CSeqDBIter	Begin () const
	Returns a sequence iterator. More...

bool	CheckOrFindOID (int &next_oid) const
	Find an included OID, incrementing next_oid if necessary. More...

EOidListType	GetNextOIDChunk (int &begin_chunk, int &end_chunk, int oid_size, vector< int > &oid_list, int *oid_state=NULL)
	Return a chunk of OIDs, and update the OID bookmark. More...

void	ResetInternalChunkBookmark ()
	Resets this object's internal chunk bookmark, which is used when the oid_state argument to GetNextOIDChunk is NULL. More...

const string &	GetDBNameList () const
	Get list of database names. More...

const CSeqDBGiList *	GetGiList () const
	Get GI list attached to this database. More...

CSeqDBIdSet	GetIdSet () const
	Get IdSet list attached to this database. More...

bool	PigToOid (int pig, int &oid) const
	Translate a PIG to an OID. More...

bool	OidToPig (int oid, int &pig) const
	Translate an OID to a PIG. More...

bool	TiToOid (Int8 ti, int &oid) const
	Translate a TI to an OID. More...

bool	OidToGi (int oid, TGi &gi) const
	Translate an OID to a GI. More...

bool	GiToOid (TGi gi, int &oid) const
	Translate a GI to an OID. More...

bool	GiToOidwFilterCheck (TGi gi, int &oid) const
	Translate a GI To an OID with filter check. More...

bool	GiToPig (TGi gi, int &pig) const
	Translate a GI to a PIG. More...

bool	PigToGi (int pig, TGi &gi) const
	Translate a PIG to a GI. More...

void	AccessionToOids (const string &acc, vector< int > &oids) const
	Translate an Accession to a list of OIDs. More...

void	AccessionsToOids (const vector< string > &accs, vector< blastdb::TOid > &oids) const

void	SeqidToOids (const CSeq_id &seqid, vector< int > &oids) const
	Translate a Seq-id to a list of OIDs. More...

bool	SeqidToOid (const CSeq_id &seqid, int &oid) const
	Translate a Seq-id to any matching OID. More...

int	GetOidAtOffset (int first_seq, Uint8 residue) const
	Find the sequence closest to the given offset into the database. More...

CRef< CBioseq >	GiToBioseq (TGi gi) const
	Get a CBioseq for a given GI. More...

CRef< CBioseq >	PigToBioseq (int pig) const
	Get a CBioseq for a given PIG. More...

CRef< CBioseq >	SeqidToBioseq (const CSeq_id &seqid) const
	Get a CBioseq for a given Seq-id. More...

void	FindVolumePaths (vector< string > &paths, bool recursive=true) const
	Find volume paths. More...

void	SetIterationRange (int oid_begin, int oid_end)
	Set Iteration Range. More...

void	GetAliasFileValues (TAliasFileValues &afv)
	Get Name/Value Data From Alias Files. More...

CRef< CSeq_data >	GetSeqData (int oid, TSeqPos begin, TSeqPos end) const
	Fetch data as a CSeq_data object. More...

void	GetSequenceAsString (int oid, CSeqUtil::ECoding coding, string &output, TSeqRange range=TSeqRange()) const
	Get a sequence in a given encoding. More...

void	GetSequenceAsString (int oid, string &output, TSeqRange range=TSeqRange()) const
	Get a sequence in a readable text encoding. More...

void	ListColumns (vector< string > &titles)
	List columns titles found in this database. More...

int	GetColumnId (const string &title)
	Get an ID number for a given column title. More...

const map< string, string > &	GetColumnMetaData (int column_id)
	Get all metadata for the specified column. More...

const string &	GetColumnValue (int column_id, const string &key)
	Look up the value for a specific column metadata key. More...

const map< string, string > &	GetColumnMetaData (int column_id, const string &volname)
	Get all metadata for the specified column. More...

void	GetColumnBlob (int col_id, int oid, CBlastDbBlob &blob)
	Fetch the data blob for the given column and oid. More...

void	GetAvailableMaskAlgorithms (vector< int > &algorithms)
	Get a list of algorithm IDs for which mask data exists. More...

int	GetMaskAlgorithmId (const string &algo_name) const
	Get the numeric algorithm ID for a string. More...

string	GetAvailableMaskAlgorithmDescriptions ()
	Returns a formatted string with the list of available masking algorithms in this database for display purposes (i.e. More...

vector< int >	ValidateMaskAlgorithms (const vector< int > &algorithm_ids)
	Validates the algorithm IDs passed to this function, returning a vector of those algorithm IDs not present in this object. More...

void	GetMaskAlgorithmDetails (int algorithm_id, objects::EBlast_filter_program &program, string &program_name, string &algo_opts)
	Get information about one type of masking available here. More...

void	GetMaskAlgorithmDetails (int algorithm_id, string &program, string &program_name, string &algo_opts)

void	GetMaskData (int oid, const vector< int > &algo_ids, TSequenceRanges &ranges)
	Get masked ranges of a sequence. More...

void	GetMaskData (int oid, int algo_id, TSequenceRanges &ranges)
	Get masked ranges of a sequence. More...

void	SetOffsetRanges (int oid, const TRangeList &offset_ranges, bool append_ranges, bool cache_data)
	Apply a range of offsets to a database sequence. More...

void	RemoveOffsetRanges (int oid)
	Remove any offset ranges for the given OID. More...

void	FlushOffsetRangeCache ()
	Flush all offset ranges cached. More...

void	SetNumberOfThreads (int num_threads, bool force_mt=false)
	Setting the number of threads. More...

Int8	GetDiskUsage () const
	Retrieve the disk usage in bytes for this BLAST database. More...

void	SetVolsMemBit (int mbit)
	Set the membership of all volumes. More...

void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Dump debug information for this object. More...

EBlastDbVersion	GetBlastDbVersion () const
	Return blast db version. More...

void	TaxIdsToOids (set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv) const
	Get Oid list for input tax ids. More...

void	GetDBTaxIds (set< TTaxId > &tax_ids) const
	Get all unique tax ids from db. More...

void	GetTaxIdsForOids (const vector< blastdb::TOid > &oids, set< TTaxId > &tax_ids) const

CRef< CBlast_db_metadata >	GetDBMetaData (string user_path=kEmptyStr)

void	GetTaxIdsForAccession (const string &accs, vector< TTaxId > &taxids)
	Get all tax ids for an accessions. More...

void	GetTaxIdsForSeqId (const CSeq_id &seq_id, vector< TTaxId > &taxids)
	Get all tax ids for a seq id. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Additional Inherited Members
Public Types inherited from CSeqDB
enum	EOidListType { eOidList , eOidRange }
	Indicates how block of OIDs was returned. More...

enum	ESeqType { eProtein , eNucleotide , eUnknown }
	Sequence types (eUnknown tries protein, then nucleotide). More...

enum	ESummaryType { eUnfilteredAll , eFilteredAll , eFilteredRange }
	Types of summary information available. More...

enum	EMmapFileTypes { eMmap_IndexFile , eMmap_SequenceFile }
	File type for which mmap strategy may be set. More...

enum	EMmapStrategies { eMmap_Normal , eMmap_Sequential , eMmap_WillNeed }
	Permitted mmap strategies. More...

typedef TSeqDBAliasFileValues	TAliasFileValues
	Import type to allow shorter name. More...

typedef int	TOID
	Sequence type accepted and returned for OID indices. More...

typedef int	TPIG
	Sequence type accepted and returned for PIG indices. More...

typedef TGi	TGI
	Sequence type accepted and returned for GI indices. More...

typedef set< pair< int, int > >	TRangeList
	List of sequence offset ranges. More...

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CSeqDB
static string	ESeqType2String (ESeqType type)
	Converts a CSeqDB sequence type into a human readable string. More...

static string	GenerateSearchPath ()
	Returns the default BLAST database search path configured for this local installation of BLAST. More...

static CRef< CBlast_def_line_set >	ExtractBlastDefline (const CBioseq &bioseq)
	Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB. More...

static CRef< CBlast_def_line_set >	ExtractBlastDefline (const CBioseq_Handle &handle)
	Extract a Blast-def-line-set object from a Bioseq_Handle retrieved by CSeqDB. More...

static CTime	GetDate (const string &dbname, ESeqType seqtype)
	Returns the construction date of the database. More...

static void	FindVolumePaths (const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)
	Find volume paths. More...

static void	GetTaxInfo (TTaxId taxid, SSeqDBTaxInfo &info)
	Get taxonomy information. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CSeqDB
static const string	kOidNotFound
	String containing the error message in exceptions thrown when a given OID cannot be found. More...

static const char *	kBlastDbDateFormat = "b d, Y H:m P"
	Format string for the date returned by CSeqDB::GetDate. More...

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CSeqDB
	CSeqDB ()
	No-argument Constructor. More...

void	x_GetDBFilesMetaData (Int8 &disk_bytes, Int8 &cached_bytes, vector< string > &db_files, const string &user_path) const

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes inherited from CSeqDB
class CSeqDBImpl *	m_Impl
	Implementation details are hidden. (See seqdbimpl.hpp). More...

Detailed Description

CSeqDBExpert.

User interface class for blast databases, including experimental and advanced code for expert NCBI use.

Definition at line 55 of file seqdbexpert.hpp.

Constructor & Destructor Documentation

◆ CSeqDBExpert() [1/3]

CSeqDBExpert::CSeqDBExpert	(	const string &	dbname,
		ESeqType	seqtype,
		CSeqDBGiList *	gilist = `0`
	)

Short Constructor.

This version of the constructor assumes memory mapping and that the entire possible OID range will be included.

Parameters

dbname	A list of database or alias names, seperated by spaces
seqtype	Specify eProtein, eNucleotide, or eUnknown.
gilist	The database will be filtered by this GI list if non-null.

Definition at line 38 of file seqdbexpert.cpp.

◆ CSeqDBExpert() [2/3]

CSeqDBExpert::CSeqDBExpert	(	const string &	dbname,
		ESeqType	seqtype,
		int	oid_begin,
		int	oid_end,
		bool	use_mmap,
		CSeqDBGiList *	gi_list = `0`
	)

Constructor with MMap Flag and OID Range.

If the oid_end value is specified as zero, or as a value larger than the number of OIDs, it will be adjusted to the number of OIDs in the database. Specifying 0,0 for the start and end will cause inclusion of the entire database. This version of the constructor is obsolete because the sequence type is specified as a character (eventually only the ESeqType version will exist).

Parameters

dbname	A list of database or alias names, seperated by spaces.
seqtype	Specify eProtein, eNucleotide, or eUnknown.
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	The database will be filtered by this GI list if non-null.

Definition at line 45 of file seqdbexpert.cpp.

◆ CSeqDBExpert() [3/3]

CSeqDBExpert::CSeqDBExpert ( )

Null Constructor.

This version of the constructor does not open a specific blast database. This is provided for cases where the application only needs 'global' resources like the taxonomy database.

Definition at line 55 of file seqdbexpert.cpp.

◆ ~CSeqDBExpert()

CSeqDBExpert::~CSeqDBExpert ( )

Destructor.

This will return resources acquired by this object, including any gotten by the GetSequence() call, whether or not they have been returned by RetSequence().

Definition at line 60 of file seqdbexpert.cpp.

Member Function Documentation

◆ GetGiBounds()

void CSeqDBExpert::GetGiBounds	(	TGi *	low_id,
		TGi *	high_id,
		int *	count
	)

Get GI Bounds.

Fetch the lowest, highest, and total number of GIs. A value is returned for each non-null argument. If the operation fails, an exception will be thrown, which probably indicates a missing index file.

Parameters

low_id	Lowest GI value in database. [out]
high_id	Highest GI value in database. [out]
count	Number of GI values in database. [out]

Definition at line 74 of file seqdbexpert.cpp.

References count, CSeqDBImpl::GetGiBounds(), and CSeqDB::m_Impl.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetPigBounds()

void CSeqDBExpert::GetPigBounds	(	int *	low_id,
		int *	high_id,
		int *	count
	)

Get PIG Bounds.

Fetch the lowest, highest, and total number of PIGs. A value is returned for each non-null argument. If the operation fails, an exception will be thrown, which probably indicates a missing index file.

Parameters

low_id	Lowest PIG value in database. [out]
high_id	Highest PIG value in database. [out]
count	Number of PIG values in database. [out]

Definition at line 83 of file seqdbexpert.cpp.

References count, CSeqDBImpl::GetPigBounds(), and CSeqDB::m_Impl.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetRawSeqAndAmbig()

void CSeqDBExpert::GetRawSeqAndAmbig	(	int	oid,
		const char **	buffer,
		int *	seq_length,
		int *	ambig_length
	)		const

Raw Sequence and Ambiguity Data.

Get a pointer to the raw sequence and ambiguity data, and the length of each. The encoding for these is not defined here and should not be relied on to be compatible between different database format versions. NULL can be supplied for parameters that are not needed (except oid). RetSequence() must be called with the pointer returned by 'buffer' if and only if that pointer is supplied as non-null by the user. Protein sequences will never have ambiguity data. Ambiguity data will be packed in the returned buffer at offset *seq_length.

Parameters

oid	Ordinal id of the sequence.
buffer	Buffer of raw data.
seq_length	Returned length of the sequence data.
ambig_length	Returned length of the ambiguity data.

Definition at line 64 of file seqdbexpert.cpp.

References buf, CSeqDBImpl::GetRawSeqAndAmbig(), and CSeqDB::m_Impl.

Referenced by BOOST_AUTO_TEST_CASE(), CRawSeqDBSource::GetNext(), CClusterDBSource::GetNext(), s_FetchRawData(), and CBuildDatabase::x_DupLocal().

◆ GetSequenceHash()

unsigned CSeqDBExpert::GetSequenceHash ( int oid )

Get the sequence hash for a given OID.

The sequence data is fetched and the sequence hash is computed and returned.

Parameters

oid	The sequence to compute the hash of. [in]

Returns: The sequence hash.

Definition at line 106 of file seqdbexpert.cpp.

References CSeqDBImpl::GetSequenceHash(), and CSeqDB::m_Impl.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetStringBounds()

void CSeqDBExpert::GetStringBounds	(	string *	low_id,
		string *	high_id,
		int *	count
	)

Get String Bounds.

Fetch the lowest, highest, and total number of string keys in the database index. A value is returned for each non-null argument. If the operation fails, an exception will be thrown, which probably indicates a missing index file. Note that the number of string keys does not directly correspond to the number of deflines, Seq-ids, or accessions.

Parameters

low_id	Lowest string value in database. [out]
high_id	Highest string value in database. [out]
count	Number of string values in database. [out]

Definition at line 92 of file seqdbexpert.cpp.

References count, CSeqDBImpl::GetStringBounds(), and CSeqDB::m_Impl.

◆ HashToOids()

void CSeqDBExpert::HashToOids	(	unsigned	hash,
		vector< int > &	oids
	)

Get the OIDs for a given sequence hash.

The OIDs corresponding to a hash value are found and returned.

Parameters

hash	The sequence hash to look up. [in]
oids	OIDs of sequences with this hash. [out]

Returns: True if the hash value was found, false otherwise.

Definition at line 115 of file seqdbexpert.cpp.

References CSeqDBImpl::HashToOids(), and CSeqDB::m_Impl.

Referenced by BOOST_AUTO_TEST_CASE().

◆ Verify()

void CSeqDBExpert::Verify ( )

Verify internal SeqDB data structures for consistency.

Definition at line 101 of file seqdbexpert.cpp.

The documentation for this class was generated from the following files:

include/objtools/blast/seqdb_reader/seqdbexpert.hpp
src/objtools/blast/seqdb_reader/seqdbexpert.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSeqDBExpert() [1/3]

◆ CSeqDBExpert() [2/3]

◆ CSeqDBExpert() [3/3]

◆ ~CSeqDBExpert()

Member Function Documentation

◆ GetGiBounds()

◆ GetPigBounds()

◆ GetRawSeqAndAmbig()

◆ GetSequenceHash()

◆ GetStringBounds()

◆ HashToOids()

◆ Verify()