CSeqDBIsam Class Reference

Search Toolkit Book for CSeqDBIsam

#include <seqdbisam.hpp>

Inheritance diagram for CSeqDBIsam:

[legend]Collaboration diagram for CSeqDBIsam:

[legend]List of all members.

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Detailed Description

CSeqDBIsam.

Manages one ISAM file, which will translate either PIGs, GIs, or Accessions to OIDs. Translation in the other direction is done in the CSeqDBVol code. Files managed by this class include those with the extensions pni, pnd, ppi, ppd, psi, psd, nsi, nsd, nni, and nnd. Each instance of this object will manage one pair of these files, including one whose name ends in 'i' and one whose name ends in 'd'.

Definition at line 60 of file seqdbisam.hpp.

Public Types
typedef CSeqDBGiList::SGiOid	TGiOid
	Import the type representing one GI, OID association.
typedef CSeqDBAtlas::TIndx	TIndx
	Type which is large enough to span the bytes of an ISAM file.
typedef int	TOid
	This class works with OIDs relative to a specific volume.
typedef int	TPig
	PIG identifiers for numeric indices over protein volumes.
typedef int	TGi
	Genomic IDs, the most common numerical identifier.
typedef Int8	TTi
	Identifier type for trace databases.
typedef Int8	TId
	Type large enough to hold any numerical ID.
enum	EIdentType {   eGiId, eTiId, ePigId, eStringId,   eHashId, eOID }
	Identifier formats used by this class. More...
enum	EIsamDbType {   eNumeric = 0, eNumericNoData = 1, eString = 2, eStringDatabase = 3,   eStringBin = 4, eNumericLongId = 5 }
	Types of database this class can access. More...
Public Member Functions
	CSeqDBIsam (CSeqDBAtlas &atlas, const string &dbname, char prot_nucl, char file_ext_char, EIdentType ident_type)
	Constructor.
	~CSeqDBIsam ()
	Destructor.
bool	PigToOid (TPig pig, TOid &oid, CSeqDBLockHold &locked)
	PIG translation.
bool	IdToOid (Int8 id, TOid &oid, CSeqDBLockHold &locked)
	GI or TI translation.
void	IdsToOids (int vol_start, int vol_end, CSeqDBGiList &ids, CSeqDBLockHold &locked)
	Translate Gis and Tis to Oids for the given ID list.
void	IdsToOids (int vol_start, int vol_end, CSeqDBNegativeList &ids, CSeqDBLockHold &locked)
	Compute list of included OIDs based on a negative ID list.
void	StringToOids (const string &acc, vector< TOid > &oids, bool adjusted, bool &version_check, CSeqDBLockHold &locked)
	String translation.
bool	SeqidToOid (const string &acc, TOid &oid, CSeqDBLockHold &locked)
	Seq-id translation.
void	HashToOids (unsigned hash, vector< TOid > &oids, CSeqDBLockHold &locked)
	Sequence hash lookup.
void	UnLease ()
	Return any memory held by this object to the atlas.
void	GetIdBounds (Int8 &low_id, Int8 &high_id, int &count, CSeqDBLockHold &locked)
	Get Numeric Bounds.
void	GetIdBounds (string &low_id, string &high_id, int &count, CSeqDBLockHold &locked)
	Get String Bounds.
Static Public Member Functions
static EIdentType	TryToSimplifyAccession (const string &acc, Int8 &num_id, string &str_id, bool &simpler)
	String id simplification.
static EIdentType	SimplifySeqid (CSeq_id &bestid, const string *acc, Int8 &num_id, string &str_id, bool &simpler)
	Seq-id simplification.
static bool	IndexExists (const string &dbname, char prot_nucl, char file_ext_char)
	Check if a given ISAM index exists.
Private Types
enum	EErrorCode {   eNotFound = 1, eNoError = 0, eBadVersion = -10, eBadType = -11,   eWrongFile = -12 }
	Exit conditions occurring in this code. More...
Private Member Functions
bool	x_IdentToOid (Int8 id, TOid &oid, CSeqDBLockHold &locked)
	Numeric identifier lookup.
EErrorCode	x_SearchIndexNumeric (Int8 Number, int *Data, Uint4 *Index, Int4 &SampleNum, bool &done, CSeqDBLockHold &locked)
	Index file search.
void	x_SearchIndexNumericMulti (int vol_start, int vol_end, CSeqDBGiList &gis, bool use_tis, CSeqDBLockHold &locked)
	GiList Translation.
void	x_SearchNegativeMulti (int vol_start, int vol_end, CSeqDBNegativeList &gis, bool use_tis, CSeqDBLockHold &locked)
	Negative ID List Translation.
EErrorCode	x_SearchDataNumeric (Int8 Number, int *Data, Uint4 *Index, Int4 SampleNum, CSeqDBLockHold &locked)
	Data file search.
void	x_SearchDataNumericMulti (int vol_start, int vol_end, CSeqDBGiList &gis, int &gilist_index, int sample_index, bool use_tis, CSeqDBLockHold &locked)
	GiList translation for one page of a data file.
EErrorCode	x_NumericSearch (Int8 Number, int *Data, Uint4 *Index, CSeqDBLockHold &locked)
	Numeric identifier lookup.
EErrorCode	x_StringSearch (const string &term_in, vector< string > &term_out, vector< string > &value_out, vector< TIndx > &index_out, CSeqDBLockHold &locked)
	String identifier lookup.
EErrorCode	x_InitSearch (CSeqDBLockHold &locked)
	Initialize the search object.
int	x_GetPageNumElements (Int4 SampleNum, Int4 *Start)
	Determine the number of elements in the data page.
bool	x_SparseStringToOids (const string &acc, vector< int > &oids, bool adjusted, CSeqDBLockHold &locked)
	Lookup a string in a sparse table.
int	x_DiffCharLease (const string &term_in, CSeqDBMemLease &lease, const string &file_name, TIndx file_length, Uint4 at_least, TIndx KeyOffset, bool ignore_case, CSeqDBLockHold &locked)
	Find the first character to differ in two strings.
int	x_DiffChar (const string &term_in, const char *begin, const char *end, bool ignore_case)
	Find the first character to differ in two strings.
void	x_ExtractData (const char *key_start, const char *entry_end, vector< string > &key_out, vector< string > &data_out)
	Extract the data from a key-value pair in memory.
TIndx	x_GetIndexKeyOffset (TIndx sample_offset, Uint4 sample_num, CSeqDBLockHold &locked)
	Get the offset of the specified sample.
void	x_GetIndexString (TIndx key_offset, int length, string &prefix, bool trim_to_null, CSeqDBLockHold &locked)
	Read a string from the index file.
int	x_DiffSample (const string &term_in, Uint4 SampleNum, TIndx &KeyOffset, CSeqDBLockHold &locked)
	Find the first character to differ in two strings.
void	x_ExtractAllData (const string &term_in, TIndx sample_index, vector< TIndx > &indices_out, vector< string > &keys_out, vector< string > &data_out, CSeqDBLockHold &locked)
	Find matches in the given page of a string ISAM file.
void	x_ExtractPageData (const string &term_in, TIndx page_index, const char *beginp, const char *endp, vector< TIndx > &indices_out, vector< string > &keys_out, vector< string > &data_out)
	Find matches in the given memory area of a string ISAM file.
void	x_LoadPage (TIndx SampleNum1, TIndx SampleNum2, const char **beginp, const char **endp, CSeqDBLockHold &locked)
	Map a page into memory.
int	x_TestNumericSample (CSeqDBMemLease &index_lease, int index, Int8 key_in, Int8 &key_out, int &data_out)
	Test a sample key value from a numeric index.
void	x_GetNumericSample (CSeqDBMemLease &index_lease, int index, Int8 &key_out, int &data_out)
	Get a sample key value from a numeric index.
bool	x_AdvanceGiList (int vol_start, int vol_end, CSeqDBGiList &gis, int &index, Int8 key, int data, bool use_tis)
	Advance the GI list.
bool	x_FindInNegativeList (CSeqDBNegativeList &ids, int &index, Int8 key, bool use_tis)
	Find ID in the negative GI list using PBS.
bool	x_AdvanceIsamIndex (CSeqDBMemLease &index_lease, int &index, Int8 target_gi, Int8 &isam_key, int &isam_data)
	Advance the ISAM file.
void	x_MapDataPage (int sample_index, int &start, int &num_elements, const void **data_page_begin, CSeqDBLockHold &locked)
	Map a data page.
void	x_GetDataElement (const void *dpage, int index, Int8 &key, int &data)
	Get a particular data element from a data page.
void	x_FindIndexBounds (CSeqDBLockHold &locked)
	Find the least and greatest keys in this ISAM file.
bool	x_OutOfBounds (Int8 key, CSeqDBLockHold &locked)
	Check whether a numeric key is within this volume's bounds.
bool	x_OutOfBounds (string key, CSeqDBLockHold &locked)
	Check whether a string key is within this volume's bounds.
Uint8	x_GetNumericKey (const void *p)
int	x_GetNumericData (const void *p)
Static Private Member Functions
static void	x_Upper (string &s)
	Converts a string to upper case.
static Int8	x_GetId (CSeqDBGiList &ids, int index, bool use_tis)
	Fetch a GI or TI from a GI list.
static Int8	x_GetOid (CSeqDBGiList &ids, int index, bool use_tis)
	Fetch an OID from the GI or TI vector in a GI list.
static Int8	x_GetId (CSeqDBNegativeList &ids, int index, bool use_tis)
	Fetch a GI or TI from a GI list.
static void	x_MakeFilenames (const string &dbname, char prot_nucl, char file_ext_char, string &index_name, string &data_name)
	Make filenames for ISAM file.
Private Attributes
CSeqDBAtlas &	m_Atlas
	The memory management layer.
EIdentType	m_IdentType
	The type of identifier this class uses.
CSeqDBMemLease	m_IndexLease
	A persistent lease on the ISAM index file.
CSeqDBMemLease	m_DataLease
	A persistent lease on the ISAM data file.
int	m_Type
	The format type of database files found (eNumeric or eString).
string	m_DataFname
	The filename of the ISAM data file.
string	m_IndexFname
	The filename of the ISAM index file.
TIndx	m_DataFileLength
	The length of the ISAM data file.
TIndx	m_IndexFileLength
	The length of the ISAM index file.
Int4	m_NumTerms
	Number of terms in database.
Int4	m_NumSamples
	Number of terms in ISAM index.
Int4	m_PageSize
	Page size of ISAM index.
Int4	m_MaxLineSize
	Maximum string length in the database.
Int4	m_IdxOption
	Options set by upper layer.
bool	m_Initialized
	Flag indicating whether initialization has been done.
TIndx	m_KeySampleOffset
	Offset of samples in index file.
bool	m_TestNonUnique
	Check if data for String ISAM sorted.
char *	m_FileStart
	Pointer to index file if no memmap.
Int4	m_FirstOffset
	First and last offset's of last page.
Int4	m_LastOffset
	First and last offset's of last page.
SIsamKey	m_FirstKey
	First volume key.
SIsamKey	m_LastKey
	Last volume key.
bool	m_LongId
	Use Uint8 for the key.
int	m_Keysize
	size of the numeric key-data
Classes
class	SIsamKey
	Stores a key for an ISAM file. More...

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Member Typedef Documentation

typedef int CSeqDBIsam::TGi

Genomic IDs, the most common numerical identifier. Definition at line 95 of file seqdbisam.hpp.

typedef CSeqDBGiList::SGiOid CSeqDBIsam::TGiOid

Import the type representing one GI, OID association. Definition at line 63 of file seqdbisam.hpp.

typedef Int8 CSeqDBIsam::TId

Type large enough to hold any numerical ID. Definition at line 101 of file seqdbisam.hpp.

typedef CSeqDBAtlas::TIndx CSeqDBIsam::TIndx

Type which is large enough to span the bytes of an ISAM file. Definition at line 86 of file seqdbisam.hpp.

typedef int CSeqDBIsam::TOid

This class works with OIDs relative to a specific volume. Definition at line 89 of file seqdbisam.hpp.

typedef int CSeqDBIsam::TPig

PIG identifiers for numeric indices over protein volumes. Definition at line 92 of file seqdbisam.hpp.

typedef Int8 CSeqDBIsam::TTi

Identifier type for trace databases. Definition at line 98 of file seqdbisam.hpp.

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Member Enumeration Documentation

enum CSeqDBIsam::EErrorCode [private]

Exit conditions occurring in this code. Enumerator: eNotFound  eNoError  The key was not found. eBadVersion  Lookup was successful. eBadType  The format version of the ISAM file is unsupported. eWrongFile  The requested ISAM type did not match the file. Definition at line 481 of file seqdbisam.hpp.

enum CSeqDBIsam::EIdentType

Identifier formats used by this class. Enumerator: eGiId  eTiId  Genomic ID is a relatively stable numeric identifier for sequences. ePigId  Trace ID is a numeric identifier for Trace sequences. eStringId  Each PIG identifier refers to exactly one protein sequence. eHashId  Some sequence sources uses string identifiers. eOID  The ordinal id indicates the order of the data in the volume's index file. Definition at line 66 of file seqdbisam.hpp.

enum CSeqDBIsam::EIsamDbType

Types of database this class can access. Enumerator: eNumeric  eNumericNoData  Numeric database with Key/Value pairs in the index file. eString  This type is not supported. eStringDatabase  String database type used here. eStringBin  This type is not supported. eNumericLongId  This type is not supported. Definition at line 76 of file seqdbisam.hpp.

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Constructor & Destructor Documentation

CSeqDBIsam::CSeqDBIsam (  CSeqDBAtlas &  atlas, const string &  dbname, char  prot_nucl, char  file_ext_char, EIdentType  ident_type )

Constructor. An ISAM file object corresponds to an index file and a data file, and converts identifiers (string, GI, or PIG) into OIDs relative to a particular database volume. Parameters: atlas  The memory management object. [in] dbname  The name of the volume's files (minus the extension). [in] prot_nucl  Whether the sequences are protein or nucleotide. [in] file_ext_char  This is 's', 'n', or 'p', for string, GI, or PIG, respectively. [in] ident_type  The type of identifiers this database translates. [in] Definition at line 1409 of file seqdbisam.cpp. References DEFAULT_NISAM_SIZE, DEFAULT_SISAM_SIZE, eGiId, eHashId, eNumeric, ePigId, eString, eStringId, eTiId, m_DataFname, m_IndexFname, m_PageSize, m_Type, NCBI_THROW, and x_MakeFilenames().

CSeqDBIsam::~CSeqDBIsam (   )

Destructor. Releases all resources associated with this object. Definition at line 1512 of file seqdbisam.cpp. References UnLease().

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Member Function Documentation

void CSeqDBIsam::GetIdBounds (  string &  low_id, string &  high_id, int &  count, CSeqDBLockHold &  locked )

Get String Bounds. Fetch the lowest, highest, and total number of string keys in the database index. If the operation fails, zero will be returned for count. Parameters: low_id  Lowest string id value in database. [out] high_id  Highest string id value in database. [out] count  Number of string id values in database. [out] locked  Lock holder object for this thread. [in] Definition at line 2238 of file seqdbisam.cpp. References eNoError, error(), CSeqDBIsam::SIsamKey::GetString(), CSeqDBIsam::SIsamKey::IsSet(), CSeqDBAtlas::Lock(), m_Atlas, m_FirstKey, m_Initialized, m_LastKey, m_NumTerms, x_FindIndexBounds(), and x_InitSearch().

void CSeqDBIsam::GetIdBounds (  Int8 &  low_id, Int8 &  high_id, int &  count, CSeqDBLockHold &  locked )

Get Numeric Bounds. Fetch the lowest, highest, and total number of numeric keys in the database index. If the operation fails, zero will be returned for count. Parameters: low_id  Lowest numeric id value in database. [out] high_id  Highest numeric id value in database. [out] count  Number of numeric id values in database. [out] locked  Lock holder object for this thread. [in] Definition at line 2213 of file seqdbisam.cpp. References eNoError, error(), CSeqDBIsam::SIsamKey::GetNumeric(), CSeqDBIsam::SIsamKey::IsSet(), CSeqDBAtlas::Lock(), m_Atlas, m_FirstKey, m_Initialized, m_LastKey, m_NumTerms, x_FindIndexBounds(), and x_InitSearch().

void CSeqDBIsam::HashToOids (  unsigned  hash, vector< TOid > &  oids, CSeqDBLockHold &  locked )

Sequence hash lookup. This methods tries to find sequences associated with a given sequence hash value. The provided value is numeric but the ISAM file uses a string format, because string searches can return multiple results per key, and there may be multiple OIDs for a given hash value due to identical sequences and collisions. Parameters: hash  The sequence hash value to look up. [in] oids  The returned oids. [out] locked  The lock hold object for this thread. [in|out] Definition at line 2263 of file seqdbisam.cpp. References _ASSERT, eHashId, eNoError, eNotFound, ITERATE, CSeqDBAtlas::Lock(), m_Atlas, m_IdentType, m_Initialized, NStr::UIntToString(), x_InitSearch(), and x_StringSearch().

void CSeqDBIsam::IdsToOids (  int  vol_start, int  vol_end, CSeqDBNegativeList &  ids, CSeqDBLockHold &  locked )

Compute list of included OIDs based on a negative ID list. This method iterates over a vector of Gis or Tis, along with the corresponding ISAM file for this volume. Each OID found in the ISAM file is marked in the negative ID list. For those for which the GI or TI is not mentioned in the negative ID list, the OID will be marked as an 'included' OID in the ID list (that OID will be searched). The OIDs for IDs that are not found in the ID list will be marked as 'visible' OIDs. When this process is done for all volumes, the SeqDB object will use all OIDs that are either marked as 'included' or NOT marked as 'visible'. The 'visible' list is needed because otherwise iteration would skip IDs that are do not have GIs or TIs (whichever is being iterated). To use this method, this volume must have an ISAM file matching the negative ID list's identifier type or an exception will be thrown. Parameters: vol_start  The starting OID of this volume. [in] vol_end  The fist OID past the end of this volume. [in] ids  The set of GI-OID pairs. [in|out] locked  The lock holder object for this thread. [in|out] Definition at line 2012 of file seqdbisam.cpp. References _ASSERT, eGiId, eTiId, CSeqDBNegativeList::GetNumGis(), CSeqDBNegativeList::InsureOrder(), CSeqDBAtlas::Lock(), m_Atlas, m_IdentType, and x_SearchNegativeMulti().

void CSeqDBIsam::IdsToOids (  int  vol_start, int  vol_end, CSeqDBGiList &  ids, CSeqDBLockHold &  locked )

Translate Gis and Tis to Oids for the given ID list. This method iterates over a vector of Gi/OID and/or Ti/OID pairs. For each pair where the OID is -1, the GI or TI will be looked up in the ISAM file, and (if found) the correct OID will be stored (otherwise the -1 will remain). This method will normally be called once for each volume. Parameters: vol_start  The starting OID of this volume. [in] vol_end  The fist OID past the end of this volume. [in] ids  The set of GI-OID or TI-OID pairs. [in|out] locked  The lock holder object for this thread. [in|out] Definition at line 1982 of file seqdbisam.cpp. References _ASSERT, CSeqDBGiList::eGi, eGiId, eTiId, CSeqDBGiList::GetNumGis(), CSeqDBGiList::InsureOrder(), CSeqDBAtlas::Lock(), m_Atlas, m_IdentType, and x_SearchIndexNumericMulti().

bool CSeqDBIsam::IdToOid (  Int8  id, TOid &  oid, CSeqDBLockHold &  locked )  [inline]

GI or TI translation. A GI or TI identifier is translated to an OID. GI identifiers are used for all types of sequences. TI identifiers are used primarily for nucleotide data in the Trace DBs. Multiple GIs may indicate the same sequence of bases and the same OID, but TIs are usually unique. Parameters: id  The GI or TI to look up. [in] oid  The returned oid. [out] locked  The lock hold object for this thread. [in|out] Returns: true if the GI was found Definition at line 168 of file seqdbisam.hpp. References _ASSERT, eGiId, eTiId, m_IdentType, and x_IdentToOid().

bool CSeqDBIsam::IndexExists (  const string &  dbname, char  prot_nucl, char  file_ext_char )  [static]

Check if a given ISAM index exists. Parameters: dbname  Base name of the database volume. prot_nucl  'n' or 'p' for protein or nucleotide. file_ext_char  Identifier symbol; 's' for string, etc. Definition at line 1502 of file seqdbisam.cpp. References x_MakeFilenames().

bool CSeqDBIsam::PigToOid (  TPig  pig, TOid &  oid, CSeqDBLockHold &  locked )  [inline]

PIG translation. A PIG identifier is translated to an OID. PIG identifiers are used exclusively for protein sequences. One PIG corresponds to exactly one sequences of amino acids, and vice versa. They are also stable; the sequence a PIG points to will never be changed. Parameters: pig  The PIG to look up. [in] oid  The returned oid. [out] locked  The lock hold object for this thread. [in|out] Returns: true if the PIG was found Definition at line 146 of file seqdbisam.hpp. References _ASSERT, ePigId, m_IdentType, and x_IdentToOid().

bool CSeqDBIsam::SeqidToOid (  const string &  acc, TOid &  oid, CSeqDBLockHold &  locked )

Seq-id translation. A Seq-id identifier (serialized to a string) is translated into an OID. This routine will attempt to simplify the seqid so as to use the faster numeric lookup techniques whenever possible. Parameters: acc  A string containing the Seq-id. [in] oid  The returned oid. [out] locked  The lock hold object for this thread. [in|out]

CSeqDBIsam::EIdentType CSeqDBIsam::SimplifySeqid (  CSeq_id &  bestid, const string *  acc, Int8 &  num_id, string &  str_id, bool &  simpler )  [static]

Seq-id simplification. Given a Seq-id, this routine devolves it to a GI or PIG if possible. If not, it formats the Seq-id into a canonical form for lookup in the string ISAM files. If the Seq-id was parsed from an accession, it can be provided in the "acc" parameter, and it will be used if the Seq-id is not in a form this code can recognize. In the case that new Seq-id types are added, support for which has not been added to this code, this mechanism will try to use the original string. Parameters: bestid  The Seq-id to look up. [in] acc  The original string the Seq-id was created from (or NULL). [in] num_id  The returned identifier, if numeric. [out] str_id  The returned identifier, if a string. [out] simpler  Whether an adjustment was done at all. [out] Returns: The resulting identifier type. Definition at line 1804 of file seqdbisam.cpp. References CDbtag_Base::CanGetDb(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbsq, eGiId, eOID, ePigId, eStringId, CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetGi(), CSeq_id_Base::GetGibbsq(), CDbtag_Base::GetTag(), NStr::UIntToString(), and CSeq_id_Base::Which(). Referenced by CSeqDBVol::SeqidToOids(), and TryToSimplifyAccession().

void CSeqDBIsam::StringToOids (  const string &  acc, vector< TOid > &  oids, bool  adjusted, bool &  version_check, CSeqDBLockHold &  locked )

String translation. A string id is translated to one or more OIDs. String ids are used by some groups which produce sequence data. In some cases, the string may correspond to more than one OID. For this reason, the OIDs are returned in a vector. The string provided is looked up in several ways. If it contains a pipe character ("|") the data will be interpreted as a SeqID. This routine can use faster lookup mechanisms if the simplification routines were able to recognize the sequence as one of several types that have numerical indices. The version_check flag is needed to support sparse indexing. If version_check is true, and the string has a version, and the lookup fails, this method will try to remove the version and search again. On return from this method version_check will be set to true if and only if the first search failed and the versionless search succeeded. CSeqDBVol::x_CheckVersions() can then be called to verify the OIDs; see that method for more information about this scenario. Parameters: acc  The string to look up. [in] oids  The returned oids. [out] adjusted  Whether the simplification adjusted the string. [in|out] version_check  If the version can be stripped [in] and if it was [out]. locked  The lock hold object for this thread. [in|out] Definition at line 1646 of file seqdbisam.cpp. References _ASSERT, eNoError, eNotFound, eStringId, CSeqDBAtlas::Lock(), m_Atlas, m_IdentType, m_Initialized, pos, x_InitSearch(), and x_StringSearch().

CSeqDBIsam::EIdentType CSeqDBIsam::TryToSimplifyAccession (  const string &  acc, Int8 &  num_id, string &  str_id, bool &  simpler )  [static]

String id simplification. This routine tries to produce a numerical type from a string identifier. SeqDB can use faster lookup mechanisms if a PIG, GI, or OID type can be recognized in the string, for example. Even when the output is a string, it may be better formed for the purpose of lookup in the string ISAM file. Parameters: acc  The string to look up. [in] num_id  The returned identifier, if numeric. [out] str_id  The returned identifier, if a string. [out] simpler  Whether an adjustment was done at all. [out] Returns: The resulting identifier type. Definition at line 1957 of file seqdbisam.cpp. References CSeq_id::BestRank(), eStringId, FindBestChoice(), s_SeqDB_ParseSeqIDs(), and SimplifySeqid(). Referenced by CSeqDBVol::AccessionToOids().

void CSeqDBIsam::UnLease (   )

Return any memory held by this object to the atlas. Definition at line 1517 of file seqdbisam.cpp. References CSeqDBMemLease::Empty(), m_Atlas, m_IndexLease, and CSeqDBAtlas::RetRegion(). Referenced by ~CSeqDBIsam().

bool CSeqDBIsam::x_AdvanceGiList (  int  vol_start, int  vol_end, CSeqDBGiList &  gis, int &  index, Int8  key, int  data, bool  use_tis )  [inline, private]

Advance the GI list. Skip over any GIs in the GI list that are less than the key, translate any that are equal to it, and skip past any GI/OID pairs that have already been translated. Uses the parabolic binary search technique. Parameters: vol_start  The starting OID of the volume. vol_end  The ending OID of the volume. gis  The GI list to advance through. index  The working index into the GI list. key  The current key in the ISAM file. data  The data corresponding to key. use_tis  Use trace IDs instead of GIs. Returns: Returns true if any advancement was possible. Definition at line 1276 of file seqdbisam.hpp. References CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumTis(), x_GetId(), and x_GetOid().

bool CSeqDBIsam::x_AdvanceIsamIndex (  CSeqDBMemLease &  index_lease, int &  index, Int8  target_gi, Int8 &  isam_key, int &  isam_data )  [inline, private]

Advance the ISAM file. Skip over any GI/OID pairs in the ISAM file that are less than the target_gi. Uses the parabolic binary search technique. Parameters: index_lease  The memory lease to use with the index file. index  The working index into the ISAM file. target_gi  The GI from the GI list for which we are searching. isam_key  The key of the current location in the ISAM file. isam_data  The data corresponding to isam_key. Returns: Returns true if any advancement was possible. Definition at line 1370 of file seqdbisam.hpp. References m_NumSamples, and x_TestNumericSample().

Int4 CSeqDBIsam::x_DiffChar (  const string &  term_in, const char *  begin, const char *  end, bool  ignore_case )  [private]

Find the first character to differ in two strings. This finds the index of the first character to differ in meaningful way between two strings. One of the strings is a term that is passed in; the other is a range of memory represented by two pointers. Parameters: term_in  The key string to compare against. begin  A pointer to the start of the second string. end  A pointer to the end of the second string. ignore_case  Whether to treat the search as case-sensitive Returns: The position of the first difference. Definition at line 857 of file seqdbisam.cpp. References ch1, ch2, and s_SeqDBIsam_NullifyEOLs(). Referenced by x_ExtractAllData(), and x_ExtractPageData().

int CSeqDBIsam::x_DiffCharLease (  const string &  term_in, CSeqDBMemLease &  lease, const string &  file_name, TIndx  file_length, Uint4  at_least, TIndx  KeyOffset, bool  ignore_case, CSeqDBLockHold &  locked )  [private]

Find the first character to differ in two strings. This finds the index of the first character to differ in meaningful way between two strings. One of the strings is a term that is passed in; the other is assumed to be located in the ISAM table, a lease to which is passed to this function. Parameters: term_in  The key string to compare against. lease  A lease to hold the data in the ISAM table file. file_name  The name of the ISAM file to work with. file_length  The length of the file named by file_name. at_least  Try to get at least this many bytes. KeyOffset  The location of the key in the leased file. ignore_case  Whether to treat the search as case-sensitive locked  The lock holder object for this thread. Returns: The position of the first difference. Definition at line 777 of file seqdbisam.cpp. References CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), and m_Atlas.

int CSeqDBIsam::x_DiffSample (  const string &  term_in, Uint4  SampleNum, TIndx &  KeyOffset, CSeqDBLockHold &  locked )  [private]

Find the first character to differ in two strings. This finds the index of the first character to differ between two strings. The first string is provided, the second is one of the sample strings, indicated by the index of that sample value. Parameters: term_in  The key string to compare against. SampleNum  Selects which sample to compare with. KeyOffset  The returned offset of the key that was used. locked  This thread's lock holder object. Definition at line 1148 of file seqdbisam.cpp. References CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFname, m_IndexLease, m_KeySampleOffset, m_NumSamples, m_PageSize, and MEMORY_ONLY_PAGE_SIZE. Referenced by x_StringSearch().

void CSeqDBIsam::x_ExtractAllData (  const string &  term_in, TIndx  sample_index, vector< TIndx > &  indices_out, vector< string > &  keys_out, vector< string > &  data_out, CSeqDBLockHold &  locked )  [private]

Find matches in the given page of a string ISAM file. This searches the area around a specific page of the data file to find all matches to term_in. The results are returned in vectors. This method may search multiple pages. Parameters: term_in  The key string to compare against. sample_index  Selects which page to search. indices_out  The index of each match. keys_out  The key of each match. data_out  The value of each match. locked  This thread's lock holder object. Definition at line 956 of file seqdbisam.cpp. References m_NumSamples, m_PageSize, s_SeqDBIsam_NullifyEOLs(), x_DiffChar(), x_ExtractPageData(), and x_LoadPage(). Referenced by x_StringSearch().

void CSeqDBIsam::x_ExtractData (  const char *  key_start, const char *  entry_end, vector< string > &  key_out, vector< string > &  data_out )  [private]

Extract the data from a key-value pair in memory. Given pointers to a location in mapped memory, and the end of the mapped data, this finds the key and data values for the object at that location. Parameters: key_start  A pointer to the beginning of the key-value pair in memory. entry_end  A pointer to the end of the mapped area of memory. key_out  A string holding the ISAM entry's key data_out  A string holding the ISAM entry's value Definition at line 1061 of file seqdbisam.cpp. References s_SeqDBIsam_NullifyEOLs(). Referenced by x_ExtractPageData(), and x_FindIndexBounds().

void CSeqDBIsam::x_ExtractPageData (  const string &  term_in, TIndx  page_index, const char *  beginp, const char *  endp, vector< TIndx > &  indices_out, vector< string > &  keys_out, vector< string > &  data_out )  [private]

Find matches in the given memory area of a string ISAM file. This searches the specified section of memory to find all matches to term_in. The results are returned in vectors. Parameters: term_in  The key string to compare against. page_index  Selects which page to search. beginp  Pointer to the start of the memory area endp  Pointer to the end of the memory area indices_out  The index of each match. keys_out  The key of each match. data_out  The value of each match. Definition at line 902 of file seqdbisam.cpp. References s_SeqDBIsam_NullifyEOLs(), x_DiffChar(), and x_ExtractData(). Referenced by x_ExtractAllData(), and x_StringSearch().

void CSeqDBIsam::x_FindIndexBounds (  CSeqDBLockHold &  locked  )  [private]

Find the least and greatest keys in this ISAM file. Definition at line 2042 of file seqdbisam.cpp. References _ASSERT, eNumeric, CSeqDBAtlas::Lock(), m_Atlas, m_FirstKey, m_LastKey, m_NumSamples, m_Type, s_SeqDBIsam_NullifyEOLs(), CSeqDBIsam::SIsamKey::SetNumeric(), CSeqDBIsam::SIsamKey::SetString(), x_ExtractData(), x_GetDataElement(), x_LoadPage(), x_MapDataPage(), and x_Upper(). Referenced by GetIdBounds(), and x_OutOfBounds().

bool CSeqDBIsam::x_FindInNegativeList (  CSeqDBNegativeList &  ids, int &  index, Int8  key, bool  use_tis )  [inline, private]

Find ID in the negative GI list using PBS. Use parabolic binary search to find the specified ID in the negative ID list. The 'index' value is the index to start the search at (this must refer to an index at or before the target data if the search is to succeed). Whether the search was successful or not, the index will be moved forward past any elements with values less than 'key'. Parameters: ids  Negative ID list. [in|out] index  Index into negative ID list. [in|out] key  Key for which to search. [in] use_tis  If true, search for a TI, else for a GI. [in] Returns: True if the search found the ID. Definition at line 1336 of file seqdbisam.hpp. References CSeqDBNegativeList::GetNumGis(), CSeqDBNegativeList::GetNumTis(), and x_GetId(). Referenced by x_SearchNegativeMulti().

void CSeqDBIsam::x_GetDataElement (  const void *  dpage, int  index, Int8 &  key, int &  data )  [inline, private]

Get a particular data element from a data page. Parameters: dpage  A pointer to that page in memory. [in] index  The index of the element to fetch. [in] key  The returned key. [out] data  The returned value. [out] Definition at line 1450 of file seqdbisam.hpp. References m_Keysize, x_GetNumericData(), and x_GetNumericKey(). Referenced by x_FindIndexBounds(), x_SearchDataNumericMulti(), and x_SearchNegativeMulti().

static Int8 CSeqDBIsam::x_GetId (  CSeqDBNegativeList &  ids, int  index, bool  use_tis )  [inline, static, private]

Fetch a GI or TI from a GI list. Definition at line 1120 of file seqdbisam.hpp. References CSeqDBNegativeList::GetGi(), and CSeqDBNegativeList::GetTi().

static Int8 CSeqDBIsam::x_GetId (  CSeqDBGiList &  ids, int  index, bool  use_tis )  [inline, static, private]

Fetch a GI or TI from a GI list. Definition at line 1104 of file seqdbisam.hpp. References CSeqDBGiList::GetGiOid(), and CSeqDBGiList::GetTiOid(). Referenced by x_AdvanceGiList(), x_FindInNegativeList(), and x_SearchDataNumericMulti().

CSeqDBIsam::TIndx CSeqDBIsam::x_GetIndexKeyOffset (  TIndx  sample_offset, Uint4  sample_num, CSeqDBLockHold &  locked )  [private]

Get the offset of the specified sample. For string ISAM indices, the index file contains a table of offsets of the index file samples. This function gets the offset of the specified sample in the index file's table. Parameters: sample_offset  The offset into the file of the set of samples. sample_num  The index of the sample to get. locked  This thread's lock holder object. Returns: The offset of the sample in the index file. Definition at line 1091 of file seqdbisam.cpp. References CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFname, and m_IndexLease. Referenced by x_StringSearch().

void CSeqDBIsam::x_GetIndexString (  TIndx  key_offset, int  length, string &  prefix, bool  trim_to_null, CSeqDBLockHold &  locked )  [private]

Read a string from the index file. Given an offset into the index file, and a maximum length, this function returns the bytes in a string object. Parameters: key_offset  The offset into the file of the first byte. length  The maximum number of bytes to get. prefix  The string in which to return the data. trim_to_null  Whether to search for a null and return only that much data. locked  This thread's lock holder object. Definition at line 1113 of file seqdbisam.cpp. References CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFname, and m_IndexLease. Referenced by x_StringSearch().

int CSeqDBIsam::x_GetNumericData (  const void *  p  )  [inline, private]

Definition at line 1221 of file seqdbisam.hpp. References SeqDB_GetStdOrd(). Referenced by x_GetDataElement(), x_GetNumericSample(), x_SearchIndexNumeric(), and x_TestNumericSample().

Uint8 CSeqDBIsam::x_GetNumericKey (  const void *  p  )  [inline, private]

Definition at line 1214 of file seqdbisam.hpp. References SeqDB_GetStdOrd(). Referenced by x_GetDataElement(), x_GetNumericSample(), x_SearchDataNumericMulti(), x_SearchIndexNumeric(), and x_TestNumericSample().

void CSeqDBIsam::x_GetNumericSample (  CSeqDBMemLease &  index_lease, int  index, Int8 &  key_out, int &  data_out )  [inline, private]

Get a sample key value from a numeric index. Given the index of a sample value, this code will get the key. If data values are stored in the index file, the corresponding data value will also be returned. The offset of the data block is computed and returned as well. Parameters: index_lease  The memory lease to use with the index file. index  The index of the sample to get. key_out  The key found will be returned here. data_out  If an exact match, the data found will be returned here. Definition at line 1259 of file seqdbisam.hpp. References CSeqDBMemLease::GetPtr(), m_KeySampleOffset, m_Keysize, x_GetNumericData(), and x_GetNumericKey().

static Int8 CSeqDBIsam::x_GetOid (  CSeqDBGiList &  ids, int  index, bool  use_tis )  [inline, static, private]

Fetch an OID from the GI or TI vector in a GI list. Definition at line 1112 of file seqdbisam.hpp. References CSeqDBGiList::GetGiOid(), and CSeqDBGiList::GetTiOid(). Referenced by x_AdvanceGiList(), and x_SearchDataNumericMulti().

Int4 CSeqDBIsam::x_GetPageNumElements (  Int4  SampleNum, Int4 *  Start )  [private]

Determine the number of elements in the data page. The number of elements is determined based on whether this is the last page and the configured page size. Parameters: SampleNum  Which data page will be searched. Start  The returned index of the start of the page. Returns: The number of elements in this data page. Definition at line 131 of file seqdbisam.cpp. References m_NumSamples, m_NumTerms, and m_PageSize. Referenced by x_MapDataPage(), and x_SearchDataNumeric().

bool CSeqDBIsam::x_IdentToOid (  Int8  id, TOid &  oid, CSeqDBLockHold &  locked )  [private]

Numeric identifier lookup. Given a numeric identifier, this routine finds the OID. Parameters: id  The GI or PIG identifier to look up. oid  The returned oid. locked  The lock holder object for this thread. Returns: true if the identifier was found. Definition at line 1527 of file seqdbisam.cpp. References eNoError, and x_NumericSearch(). Referenced by IdToOid(), and PigToOid().

CSeqDBIsam::EErrorCode CSeqDBIsam::x_InitSearch (  CSeqDBLockHold &  locked  )  [private]

Initialize the search object. The first identifier search sets up the object by calling this function, which reads the metadata from the index file and sets all the fields needed for ISAM lookups. Parameters: locked  The lock holder object for this thread. Returns: A non-zero error on failure, or eNoError on success. Definition at line 64 of file seqdbisam.cpp. References eBadType, eBadVersion, eNoError, eNumeric, eNumericLongId, eWrongFile, CSeqDBAtlas::GetFileSize(), CSeqDBMemLease::GetPtr(), CSeqDBAtlas::GetRegion(), ISAM_VERSION, CSeqDBAtlas::Lock(), m_Atlas, m_DataFileLength, m_DataFname, m_IdxOption, m_IndexFileLength, m_IndexFname, m_IndexLease, m_Initialized, m_KeySampleOffset, m_Keysize, m_LongId, m_MaxLineSize, m_NumSamples, m_NumTerms, m_PageSize, m_Type, MEMORY_ONLY_PAGE_SIZE, and SeqDB_GetStdOrd(). Referenced by GetIdBounds(), HashToOids(), StringToOids(), x_SearchIndexNumeric(), x_SearchIndexNumericMulti(), x_SearchNegativeMulti(), and x_StringSearch().

void CSeqDBIsam::x_LoadPage (  TIndx  SampleNum1, TIndx  SampleNum2, const char **  beginp, const char **  endp, CSeqDBLockHold &  locked )  [private]

Map a page into memory. Given two indices, this method maps into memory the area starting at the beginning of the first index and extending to the end of the other. (If the indices are equal, only one page would be mapped.) Parameters: SampleNum1  The first page index. SampleNum2  The second page index. beginp  The returned starting offset of the mapped area. endp  The returned ending offset of the mapped area. locked  This thread's lock holder object. Definition at line 1193 of file seqdbisam.cpp. References _ASSERT, CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFname, m_IndexLease, and m_KeySampleOffset. Referenced by x_ExtractAllData(), x_FindIndexBounds(), and x_StringSearch().

void CSeqDBIsam::x_MakeFilenames (  const string &  dbname, char  prot_nucl, char  file_ext_char, string &  index_name, string &  data_name )  [static, private]

Make filenames for ISAM file. Parameters: dbname  Base name of the database volume. [in] prot_nucl  'n' or 'p' for protein or nucleotide. [in] file_ext_char  Identifier symbol; 's' for string, etc. [in] index_name  Filename of ISAM index file. [out] data_name  Filename of ISAM data file. [out] Definition at line 1474 of file seqdbisam.cpp. References NCBI_THROW. Referenced by CSeqDBIsam(), and IndexExists().

void CSeqDBIsam::x_MapDataPage (  int  sample_index, int &  start, int &  num_elements, const void **  data_page_begin, CSeqDBLockHold &  locked )  [inline, private]

Map a data page. The caller provides an index into the sample file. The page of data is mapped, and a pointer is returned. In addition, the starting index (start) of the data is returned, along with the number of elements in that page. Parameters: sample_index  Index into the index (i.e. pni) file. [in] start  Index of first element of the page. [out] num_elements  Number of elements in the page. [out] data_page_begin  Pointer to the returned data. [out] locked  The lock holder object for this thread. [out] Definition at line 1425 of file seqdbisam.hpp. References CSeqDBMemLease::Contains(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_DataFname, m_DataLease, m_Keysize, and x_GetPageNumElements(). Referenced by x_FindIndexBounds(), x_SearchDataNumericMulti(), and x_SearchNegativeMulti().

CSeqDBIsam::EErrorCode CSeqDBIsam::x_NumericSearch (  Int8  Number, int *  Data, Uint4 *  Index, CSeqDBLockHold &  locked )  [private]

Numeric identifier lookup. Given a numeric identifier, this routine finds the OID. Parameters: Number  The GI or PIG identifier to look up. Data  The returned OID. Index  The returned location in the ISAM table, or NULL. locked  The lock holder object for this thread. Returns: A non-zero error on failure, or eNoError on success. Definition at line 759 of file seqdbisam.cpp. References error(), x_SearchDataNumeric(), and x_SearchIndexNumeric(). Referenced by x_IdentToOid().

bool CSeqDBIsam::x_OutOfBounds (  string  key, CSeqDBLockHold &  locked )  [private]

Check whether a string key is within this volume's bounds. Parameters: key  The key for which to do the check. locked  The lock holder object for this thread. Definition at line 2188 of file seqdbisam.cpp. References CSeqDBIsam::SIsamKey::IsSet(), m_FirstKey, and x_FindIndexBounds().

bool CSeqDBIsam::x_OutOfBounds (  Int8  key, CSeqDBLockHold &  locked )  [private]

Check whether a numeric key is within this volume's bounds. Parameters: key  The key for which to do the check. locked  The lock holder object for this thread. Definition at line 2165 of file seqdbisam.cpp. References CSeqDBIsam::SIsamKey::IsSet(), m_FirstKey, and x_FindIndexBounds(). Referenced by x_SearchIndexNumeric(), and x_StringSearch().

CSeqDBIsam::EErrorCode CSeqDBIsam::x_SearchDataNumeric (  Int8  Number, int *  Data, Uint4 *  Index, Int4  SampleNum, CSeqDBLockHold &  locked )  [private]

Data file search. Given a numeric identifier, this routine finds the OID in the data file. Parameters: Number  The GI or PIG identifier to look up. Data  The returned OID. Index  The returned location in the ISAM table, or NULL. SampleNum  The location of the page in the data file to search. locked  The lock holder object for this thread. Returns: A non-zero error on failure, or eNoError on success. Definition at line 514 of file seqdbisam.cpp. References _ASSERT, CSeqDBMemLease::Contains(), eNumericNoData, CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_DataFname, m_DataLease, m_Keysize, m_Type, and x_GetPageNumElements(). Referenced by x_NumericSearch().

void CSeqDBIsam::x_SearchDataNumericMulti (  int  vol_start, int  vol_end, CSeqDBGiList &  gis, int &  gilist_index, int  sample_index, bool  use_tis, CSeqDBLockHold &  locked )  [private]

GiList translation for one page of a data file. Given a GI list, this routine finds the OID for each GI in the list using the mappings in one page of the data file. It updates the provided GI list index to skip past any GIs it translates. Parameters: vol_start  The starting OID for this ISAM file's database volume. vol_end  The fist OID past the end of this volume. gis  The GI list to translate. gilist_index  The index of the first unexamined GI in the GI list. sample_index  Indicates which data page should be used. use_tis  Use trace IDs instead of GIs. locked  The lock holder object for this thread. Definition at line 588 of file seqdbisam.cpp. References _ASSERT, eNumericNoData, CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumTis(), CSeqDBAtlas::Lock(), m_Atlas, m_Keysize, m_Type, x_GetDataElement(), x_GetId(), x_GetNumericKey(), x_GetOid(), and x_MapDataPage().

CSeqDBIsam::EErrorCode CSeqDBIsam::x_SearchIndexNumeric (  Int8  Number, int *  Data, Uint4 *  Index, Int4 &  SampleNum, bool &  done, CSeqDBLockHold &  locked )  [private]

Index file search. Given a numeric identifier, this routine finds the OID or the page in the data file where the OID can be found. Parameters: Number  The GI or PIG identifier to look up. Data  The returned OID. Index  The returned location in the ISAM table, or NULL. SampleNum  The returned location in the data file if not done. done  true if the OID was found. locked  The lock holder object for this thread. Returns: A non-zero error on failure, or eNoError on success. Definition at line 148 of file seqdbisam.cpp. References _ASSERT, CSeqDBMemLease::Contains(), eNoError, eNotFound, eNumericNoData, error(), CSeqDBMemLease::GetPtr(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFname, m_IndexLease, m_Initialized, m_KeySampleOffset, m_Keysize, m_NumSamples, m_PageSize, m_Type, x_GetNumericData(), x_GetNumericKey(), x_InitSearch(), and x_OutOfBounds(). Referenced by x_NumericSearch().

void CSeqDBIsam::x_SearchIndexNumericMulti (  int  vol_start, int  vol_end, CSeqDBGiList &  gis, bool  use_tis, CSeqDBLockHold &  locked )  [private]

GiList Translation. Given a GI list, this routine finds the OID for each ID in the list not already having a translation. Parameters: vol_start  The starting OID for this ISAM file's database volume. vol_end  The ending OID for this ISAM file's database volume. gis  The GI list to translate. use_tis  Iterate over the TI part of the GI list. locked  The lock holder object for this thread. Definition at line 242 of file seqdbisam.cpp. References CSeqDBMemLease::Contains(), eNoError, error(), CSeqDBAtlas::GetRegion(), CSeqDBAtlas::Lock(), m_Atlas, m_IndexFileLength, m_IndexFname, m_Initialized, NCBI_THROW, and x_InitSearch(). Referenced by IdsToOids().

void CSeqDBIsam::x_SearchNegativeMulti (  int  vol_start, int  vol_end, CSeqDBNegativeList &  gis, bool  use_tis, CSeqDBLockHold &  locked )  [private]

Negative ID List Translation. Given a Negative ID list, this routine turns on the bits for the OIDs found in the volume but not in the negated ID list. Parameters: vol_start  The starting OID for this ISAM file's database volume. vol_end  The ending OID for this ISAM file's database volume. gis  The Negative ID list to translate. use_tis  Iterate over TIs if true (GIs otherwise). locked  The lock holder object for this thread. Definition at line 417 of file seqdbisam.cpp. References _ASSERT, CSeqDBNegativeList::AddIncludedOid(), CSeqDBNegativeList::AddVisibleOid(), eNoError, eNumericNoData, error(), CSeqDBNegativeList::GetNumGis(), CSeqDBNegativeList::GetNumTis(), CSeqDBAtlas::Lock(), m_Atlas, m_Initialized, m_NumSamples, m_Type, NCBI_THROW, x_FindInNegativeList(), x_GetDataElement(), x_InitSearch(), and x_MapDataPage(). Referenced by IdsToOids().

bool CSeqDBIsam::x_SparseStringToOids (  const string &  acc, vector< int > &  oids, bool  adjusted, CSeqDBLockHold &  locked )  [private]

Lookup a string in a sparse table. This does string lookup in a sparse string table. There is no support (code) for this since there are currently no examples of this kind of table to test against. Parameters: acc  The string to look up. oids  The returned oids found by the search. adjusted  Whether the key was changed by the identifier simplification logic. locked  The lock holder object for this thread. Returns: true if results were found Definition at line 1793 of file seqdbisam.cpp. References _TROUBLE.

CSeqDBIsam::EErrorCode CSeqDBIsam::x_StringSearch (  const string &  term_in, vector< string > &  term_out, vector< string > &  value_out, vector< TIndx > &  index_out, CSeqDBLockHold &  locked )  [private]

String identifier lookup. Given a string identifier, this routine finds the OID(s). Parameters: term_in  The string identifier to look up. term_out  The returned keys (as strings). value_out  The returned oids (as strings). index_out  The locations where the matches were found. locked  The lock holder object for this thread. Returns: A non-zero error on failure, or eNoError on success. Definition at line 1237 of file seqdbisam.cpp. References NStr::CompareNocase(), eNoError, eNotFound, error(), CSeqDBMemLease::GetPtr(), m_IndexFileLength, m_IndexLease, m_Initialized, m_KeySampleOffset, m_MaxLineSize, m_NumSamples, m_PageSize, MEMORY_ONLY_PAGE_SIZE, x_DiffSample(), x_ExtractAllData(), x_ExtractPageData(), x_GetIndexKeyOffset(), x_GetIndexString(), x_InitSearch(), x_LoadPage(), and x_OutOfBounds(). Referenced by HashToOids(), and StringToOids().

int CSeqDBIsam::x_TestNumericSample (  CSeqDBMemLease &  index_lease, int  index, Int8  key_in, Int8 &  key_out, int &  data_out )  [inline, private]

Test a sample key value from a numeric index. This method reads the key value of an index file sample element from a numeric index file. The calling code should insure that the data is mapped in, and that the file type is correct. The key value found will be compared to the search key. This method will return 0 for an exact match, -1 if the key is less than the sample, or 1 if the key is greater. If the match is exact, it will also return the data in data_out. Parameters: index_lease  The memory lease to use with the index file. index  The index of the sample to get. key_in  The key for which the user is searching. key_out  The key found will be returned here. data_out  If an exact match, the data found will be returned here. Returns: -1, 0 or 1 when key_in is less, equal greater than key_out. Definition at line 1230 of file seqdbisam.hpp. References CSeqDBMemLease::GetPtr(), m_KeySampleOffset, m_Keysize, x_GetNumericData(), and x_GetNumericKey(). Referenced by x_AdvanceIsamIndex().

static void CSeqDBIsam::x_Upper (  string &  s  )  [inline, static, private]

Converts a string to upper case. Definition at line 1096 of file seqdbisam.hpp. Referenced by x_FindIndexBounds().

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Member Data Documentation

CSeqDBAtlas& CSeqDBIsam::m_Atlas [private]

The memory management layer. Definition at line 1143 of file seqdbisam.hpp. Referenced by GetIdBounds(), HashToOids(), IdsToOids(), StringToOids(), UnLease(), x_DiffCharLease(), x_DiffSample(), x_FindIndexBounds(), x_GetIndexKeyOffset(), x_GetIndexString(), x_InitSearch(), x_LoadPage(), x_MapDataPage(), x_SearchDataNumeric(), x_SearchDataNumericMulti(), x_SearchIndexNumeric(), x_SearchIndexNumericMulti(), and x_SearchNegativeMulti().

TIndx CSeqDBIsam::m_DataFileLength [private]

The length of the ISAM data file. Definition at line 1164 of file seqdbisam.hpp. Referenced by x_InitSearch().

string CSeqDBIsam::m_DataFname [private]

The filename of the ISAM data file. Definition at line 1158 of file seqdbisam.hpp. Referenced by CSeqDBIsam(), x_InitSearch(), x_MapDataPage(), and x_SearchDataNumeric().

CSeqDBMemLease CSeqDBIsam::m_DataLease [private]

A persistent lease on the ISAM data file. Definition at line 1152 of file seqdbisam.hpp. Referenced by x_MapDataPage(), and x_SearchDataNumeric().

char* CSeqDBIsam::m_FileStart [private]

Pointer to index file if no memmap. Definition at line 1194 of file seqdbisam.hpp.

SIsamKey CSeqDBIsam::m_FirstKey [private]

First volume key. Definition at line 1203 of file seqdbisam.hpp. Referenced by GetIdBounds(), x_FindIndexBounds(), and x_OutOfBounds().

Int4 CSeqDBIsam::m_FirstOffset [private]

First and last offset's of last page. Definition at line 1197 of file seqdbisam.hpp.

EIdentType CSeqDBIsam::m_IdentType [private]

The type of identifier this class uses. Definition at line 1146 of file seqdbisam.hpp. Referenced by HashToOids(), IdsToOids(), IdToOid(), PigToOid(), and StringToOids().

Int4 CSeqDBIsam::m_IdxOption [private]

Options set by upper layer. Definition at line 1182 of file seqdbisam.hpp. Referenced by x_InitSearch().

TIndx CSeqDBIsam::m_IndexFileLength [private]

The length of the ISAM index file. Definition at line 1167 of file seqdbisam.hpp. Referenced by x_InitSearch(), x_SearchIndexNumericMulti(), and x_StringSearch().

string CSeqDBIsam::m_IndexFname [private]

The filename of the ISAM index file. Definition at line 1161 of file seqdbisam.hpp. Referenced by CSeqDBIsam(), x_DiffSample(), x_GetIndexKeyOffset(), x_GetIndexString(), x_InitSearch(), x_LoadPage(), x_SearchIndexNumeric(), and x_SearchIndexNumericMulti().

CSeqDBMemLease CSeqDBIsam::m_IndexLease [private]

A persistent lease on the ISAM index file. Definition at line 1149 of file seqdbisam.hpp. Referenced by UnLease(), x_DiffSample(), x_GetIndexKeyOffset(), x_GetIndexString(), x_InitSearch(), x_LoadPage(), x_SearchIndexNumeric(), and x_StringSearch().

bool CSeqDBIsam::m_Initialized [private]

Flag indicating whether initialization has been done. Definition at line 1185 of file seqdbisam.hpp. Referenced by GetIdBounds(), HashToOids(), StringToOids(), x_InitSearch(), x_SearchIndexNumeric(), x_SearchIndexNumericMulti(), x_SearchNegativeMulti(), and x_StringSearch().

TIndx CSeqDBIsam::m_KeySampleOffset [private]

Offset of samples in index file. Definition at line 1188 of file seqdbisam.hpp. Referenced by x_DiffSample(), x_GetNumericSample(), x_InitSearch(), x_LoadPage(), x_SearchIndexNumeric(), x_StringSearch(), and x_TestNumericSample().

int CSeqDBIsam::m_Keysize [private]

size of the numeric key-data Definition at line 1212 of file seqdbisam.hpp. Referenced by x_GetDataElement(), x_GetNumericSample(), x_InitSearch(), x_MapDataPage(), x_SearchDataNumeric(), x_SearchDataNumericMulti(), x_SearchIndexNumeric(), and x_TestNumericSample().

SIsamKey CSeqDBIsam::m_LastKey [private]

Last volume key. Definition at line 1206 of file seqdbisam.hpp. Referenced by GetIdBounds(), and x_FindIndexBounds().

Int4 CSeqDBIsam::m_LastOffset [private]

First and last offset's of last page. Definition at line 1200 of file seqdbisam.hpp.

bool CSeqDBIsam::m_LongId [private]

Use Uint8 for the key. Definition at line 1209 of file seqdbisam.hpp. Referenced by x_InitSearch().

Int4 CSeqDBIsam::m_MaxLineSize [private]

Maximum string length in the database. Definition at line 1179 of file seqdbisam.hpp. Referenced by x_InitSearch(), and x_StringSearch().

Int4 CSeqDBIsam::m_NumSamples [private]

Number of terms in ISAM index. Definition at line 1173 of file seqdbisam.hpp. Referenced by x_AdvanceIsamIndex(), x_DiffSample(), x_ExtractAllData(), x_FindIndexBounds(), x_GetPageNumElements(), x_InitSearch(), x_SearchIndexNumeric(), x_SearchNegativeMulti(), and x_StringSearch().

Int4 CSeqDBIsam::m_NumTerms [private]

Number of terms in database. Definition at line 1170 of file seqdbisam.hpp. Referenced by GetIdBounds(), x_GetPageNumElements(), and x_InitSearch().

Int4 CSeqDBIsam::m_PageSize [private]

Page size of ISAM index. Definition at line 1176 of file seqdbisam.hpp. Referenced by CSeqDBIsam(), x_DiffSample(), x_ExtractAllData(), x_GetPageNumElements(), x_InitSearch(), x_SearchIndexNumeric(), and x_StringSearch().

bool CSeqDBIsam::m_TestNonUnique [private]

Check if data for String ISAM sorted. Definition at line 1191 of file seqdbisam.hpp.

int CSeqDBIsam::m_Type [private]

The format type of database files found (eNumeric or eString). Definition at line 1155 of file seqdbisam.hpp. Referenced by CSeqDBIsam(), x_FindIndexBounds(), x_InitSearch(), x_SearchDataNumeric(), x_SearchDataNumericMulti(), x_SearchIndexNumeric(), and x_SearchNegativeMulti().

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

• src/objtools/blast/seqdb_reader/seqdbisam.hpp
• src/objtools/blast/seqdb_reader/seqdbisam.cpp

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