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NCBI C++ ToolKit: include/objtools/blast/seqdb_reader/seqdbcommon.hpp Source File

: gi(gi_in), oid(oid_in)

: ti(ti_in), oid(oid_in)

(

&si_in =

,

oid_in = -1)

:

(si_in), oid(oid_in)

: pig(pig_in), oid(oid_in)

InsureOrder(ESortOrder order);

GiToOid(

gi,

& oid);

GiToOid(

gi,

& oid,

& index);

FindTi(

ti)

;

TiToOid(

ti,

& oid);

TiToOid(

ti,

& oid,

& index);

FindSi(

&

)

;

SiToOid(

&

,

& oid);

SiToOid(

&

,

& oid,

& index);

FindId(

&

);

m_GisOids[index];

m_TisOids[index];

m_SisOids[index];

m_PigsOids[index];

(

) m_GisOids.size();

(

) m_TisOids.size();

(

) m_SisOids.size();

(

) m_TaxIdsOids.tax_ids.size();

(

) m_TaxIdsOids.oids.size();

(

) m_PigsOids.size();

! (GetNumGis() || GetNumSis() || GetNumTis() || GetNumTaxIds() || GetNumPigs() || GetMaskOpts());

(GetNumGis() || GetNumSis() || GetNumTis());

m_GisOids[index].oid = oid;

m_TisOids[index].oid = oid;

m_SisOids[index].oid = oid;

m_PigsOids[index].oid = oid;

(

) m_GisOids.size();

(

) m_GisOids.size();

(

, m_GisOids[index].gi);

(m_GisOids[index].oid != -1);

m_GisOids[index].oid = oid;

GetGiList(vector<TGi>& gis)

;

GetTiList(vector<TTi>& tis)

;

GetSiList(vector<string>& sis)

;

GetPigList(vector<TPig>& pigs)

;

m_TaxIdsOids.tax_ids;

m_TaxIdsOids.oids;

m_TaxIdsOids.oids.clear();

m_TaxIdsOids.oids;

m_GisOids.push_back(gi);

m_TisOids.push_back(ti);

m_SisOids.push_back(

);

(vector<TPig>, itr, list) {

m_PigsOids.push_back(*itr);

m_PigsOids.push_back(pig);

m_GisOids.reserve(

);

m_TisOids.reserve(

);

m_SisOids.reserve(

);

m_PigsOids.reserve(

);

PreprocessIdsForISAMSiLookup();

m_ListInfo = list_info;

(vector<string>, itr, new_list) {

m_SisOids.push_back(*itr);

m_MaskOpts|=mask_opts;

CSeqDBGiList::GetSize<TTi>()

CSeqDBGiList::GetKey<TTi>(

index)

CSeqDBGiList::IsValueSet<TTi>(

index)

CSeqDBGiList::SetValue<TTi>(

index,

oid)

CSeqDBGiList::GetSize<string>()

CSeqDBGiList::GetKey<string>(

index)

CSeqDBGiList::IsValueSet<string>(

index)

CSeqDBGiList::SetValue<string>(

index,

oid)

CSeqDBGiList::GetSize<TPig>()

CSeqDBGiList::GetKey<TPig>(

index)

CSeqDBGiList::IsValueSet<TPig>(

index)

CSeqDBGiList::SetValue<TPig>(

index,

oid)

x_GetBit(oid);

bits = 8*

(

);

need = (num + bits - 1)/bits;

((

)m_Bitmap.size() < need) {

(new_size < need) {

m_Bitmap.resize(new_size);

bits = 8*

(

);

m_Bitmap[num/bits] |= (1 << (num % bits));

bits = 8*

(

);

!! (m_Bitmap[num/bits] & (1 << (num % bits)));

bits = 8*

(

);

m_Bitmap[num/bits] &= ~(1 << (num % bits));

m_Sis.push_back(

);

FindTi(

ti);

FindSi(

);

FindId(

&

,

& match_type);

FindId(

&

);

(

index)

(

) m_Gis.size();

(

) m_Tis.size();

(

) m_Sis.size();

(

) m_Pigs.size();

(GetNumGis() > 0);

(GetNumTis() > 0);

(GetNumSis() > 0);

= GetNumGis();

(GetNumGis() || GetNumSis() || GetNumTis());

! (GetNumGis() || GetNumTis() || GetNumSis()|| GetNumTaxIds() || GetNumPigs());

m_Included.SetBit(oid);

m_Visible.SetBit(oid);

m_Included.GetBit(oid) || (! m_Visible.GetBit(oid));

(m_Visible.Size(), m_Included.Size());

m_Gis.reserve( new_list.size() );

m_Pigs.reserve( new_list.size() );

m_Sis.reserve( new_list.size() );

(

)m_Gis.size();

PreprocessIdsForISAMSiLookup();

m_ListInfo = list_info;

m_TaxIds.insert(tax_ids.

(), tax_ids.

());

(

) m_TaxIds.size();

vector<CSeqDBGiList::SGiOid> & gis,

* in_order = 0);

vector<CSeqDBGiList::STiOid> & tis,

* in_order = 0);

vector<CSeqDBGiList::SSiOid> & sis,

* in_order = 0);

vector<CSeqDBGiList::SGiOid> & gis,

vector<CSeqDBGiList::STiOid> & tis,

vector<CSeqDBGiList::SSiOid> & sis,

vector<CSeqDBGiList::SPigOid> & pigs,

* in_order = 0);

vector<CTempString> & dbs,

keep_quote =

);

vector<CSeqDBGiList::SGiOid> & gis,

* in_order = 0);

vector<CSeqDBGiList::STiOid> & tis,

* in_order = 0);

vector<CSeqDBGiList::SSiOid> & sis,

vector<CSeqDBGiList::SGiOid> & gis,

vector<CSeqDBGiList::STiOid> & tis,

vector<CSeqDBGiList::SSiOid> & sis,

vector<CSeqDBGiList::SPigOid> & pigs,

* in_order = 0);

* in_order = 0);

(vector<Int4>, iter, ids) {

(vector<Uint8>, iter, ids) {

(vector<string>, iter, ids) {

.push_back((

) *iter);

(vector<TGi>, iter, ids) {

vector<Int8> &

()

=

.size();

vector<int> & ids,

vector<Int8> & ids,

vector<Uint8> & ids,

Blank()

;

x_SortAndUnique(vector<Int8> & ids);

x_SortAndUnique(vector<string> & ids);

x_SummarizeBooleanOp(EOperation op,

x_BooleanSetOperation(EOperation op,

vector<Int8> &

,

vector<Int8> &

,

<<

<< rhs.

;

dbtype =

);

& volpath2);

vector<string>& extensions,

vector<string>& extn);

GI list containing the intersection of two other lists of GIs.

void x_ClearBit(int num)

Clear a specific bit (to 0).

virtual ~CSeqDBBitVector()

Destructor.

vector< TBits > m_Bitmap

Bit vector.

void ClearBit(int oid)

Set the inclusion of an OID.

bool GetBit(int oid)

Get the inclusion status of an OID.

CSeqDBBitVector(const CSeqDBBitVector &other)

Prevent copy constructor.

void x_Resize(int num)

Resize the OID list.

void x_SetBit(int num)

Set a specific bit (to 1).

CSeqDBBitVector()

Constructor.

bool x_GetBit(int num)

Set a specific bit (to 1).

int Size() const

Get the size of the OID array.

int TBits

Bit vector element.

void SetBit(int oid)

Set the inclusion of an OID.

CSeqDBBitVector & operator=(const CSeqDBBitVector &other)

Prevent assignment.

int m_Size

Maximum enabled OID plus one.

@ eFileErr

Files were missing or contents were incorrect.

@ eVersionErr

DB version error.

@ eTaxidErr

No Tax Id Found.

@ eArgErr

Argument validation failed.

@ eTooManyOpenFiles

Too many open files.

@ eMemErr

Memory allocation failed.

NCBI_EXCEPTION_DEFAULT(CSeqDBException, CException)

Include standard NCBI exception behavior.

vector< SGiOid > & GetGiList()

Get list of GIs and OIDs.

void AddTi(TTi ti)

Add a new TI to the list.

vector< SGiOid > m_GisOids

Pairs of GIs and OIDs.

int GetNumGis() const

Get the number of GIs in the array.

bool PigToOid(TPig pig, int &oid, int &index)

void SetPigList(const vector< TPig > &list)

const SGiOid & GetGiOid(int index) const

Access an element of the array.

vector< SPigOid > m_PigsOids

int GetNumSis() const

Get the number of Seq-ids in the array.

const SPigOid & GetPigOid(int index) const

void AddSi(const string &si)

Add a new SeqId to the list.

vector< SPigOid > & GetPigList()

Get list og Pigs and OIDs.

bool FindPig(TPig pig) const

int GetNumTis() const

Get the number of TIs in the array.

bool IsValueSet(int index) const

vector< STiOid > m_TisOids

Pairs of GIs and OIDs.

const SSiOid & GetSiOid(int index) const

Access an element of the array.

void SetPigTranslation(int index, int oid)

vector< STiOid > & GetTiList()

Get list of Tis and OIDs.

int GetNumOidsForTaxIdList() const

void AddTaxIds(const set< TTaxId > &tax_ids)

void SetSiTranslation(int index, int oid)

Specify the correct OID for a Seq-id.

T GetKey(int index) const

Uint8 GetMaskOpts() const

SBlastSeqIdListInfo m_ListInfo

CSeqDBGiList(const CSeqDBGiList &other)

Prevent copy constructor.

void SetSiList(const vector< string > &new_list)

void SetTiTranslation(int index, int oid)

Specify the correct OID for a TI.

void SetListInfo(const SBlastSeqIdListInfo &list_info)

TODO Reserve space for seqids?

void SetValue(int index, int oid)

ESortOrder

Possible sorting states.

@ eNone

The array is unsorted or the sortedness is unknown.

void AddGi(TGi gi)

Add a new GI to the list.

void ReserveGis(size_t n)

Reserve space for GIs.

vector< SSiOid > & GetSiList()

Get list of Seq-ids and OIDs.

const vector< blastdb::TOid > & GetOidsForTaxIdsList()

virtual ~CSeqDBGiList()

Destructor.

void ReserveTis(size_t n)

Reserve space for TIs.

vector< blastdb::TOid > & SetOidsForTaxIdsList()

bool NotEmpty() const

Return true if there are elements present.

const SBlastSeqIdListInfo & GetListInfo()

set< TTaxId > & GetTaxIdsList()

void ReservePigs(size_t n)

CSeqDBGiList & operator=(const CSeqDBGiList &other)

Prevent assignment.

const STiOid & GetTiOid(int index) const

Access an element of the array.

void SetMaskOpts(EOidMaskType mask_opts)

void ReserveSis(size_t n)

void SetGiTranslation(int index, int oid)

Specify the correct OID for a GI.

bool Empty() const

Return false if there are elements present.

bool HasIdFilters() const

vector< SSiOid > m_SisOids

Pairs of Seq-ids and OIDs.

ESortOrder m_CurrentOrder

Indicates the current sort order, if any, of this container.

bool PigToOid(TPig pig, int &oid)

Helper class to allow copy-on-write semantics for CSeqDBIdSet.

CSeqDBIdSet_Vector(const vector< Uint8 > &ids)

Construct from an 'Uint8' set.

const vector< Int8 > & Get() const

Access the Int8 set.

CSeqDBIdSet_Vector(const vector< Int4 > &ids)

Construct from an 'int' set.

CSeqDBIdSet_Vector & operator=(CSeqDBIdSet_Vector &)

Prevent copy assignment.

vector< string > m_SeqIds

vector< Int8 > m_Ids

The actual list elements.

CSeqDBIdSet_Vector(CSeqDBIdSet_Vector &)

Prevent copy construction.

size_t Size() const

Get the number of elements stored here.

vector< Int8 > & Set()

Access the Int8 set.

CSeqDBIdSet_Vector(const vector< TGi > &ids)

Construct from a 'TGi' set when NCBI_STRICT_GI is in force.

CSeqDBIdSet_Vector(const vector< string > &ids)

vector< string > & SetSeqIDs()

Access the string set.

const vector< string > & GetSeqIDs() const

Access the string set.

CSeqDBIdSet_Vector(const vector< Int8 > &ids)

Construct from an 'Int8' set.

CSeqDBIdSet_Vector()

Default constructor.

SeqDB ID list for performing boolean set operations.

CRef< CSeqDBNegativeList > m_CachedNegative

Cached negative list.

CRef< CSeqDBIdSet_Vector > m_Ids

Ids stored here.

CRef< CSeqDBGiList > m_CachedPositive

Cached positive list.

virtual ~CSeqDBIdSet()

Virtual destructor.

bool m_Positive

True if the current list is positive.

EIdType

Type of IDs stored here.

EOperation

Types of operations that may be performed on GI lists.

void Compute(EOperation op, const vector< int > &ids, bool positive=true)

Perform a logical operation on a list.

bool IsPositive()

Checks whether a positive GI list was produced.

EIdType m_IdType

Id type.

void AddTaxIds(const set< TTaxId > &tax_ids)

CSeqDBBitVector m_Included

Included OID bitmap.

void AddSi(const string &si)

Add a new SeqId to the list.

void AddGi(TGi gi)

Add a new GI to the list.

CSeqDBNegativeList()

Constructor.

virtual ~CSeqDBNegativeList()

Destructor.

const vector< string > & GetSiList()

const SBlastSeqIdListInfo & GetListInfo()

void SetGiList(const vector< TGi > &new_list)

Set ID set for this negative list.

void ReserveGis(size_t n)

Reserve space for GIs.

const vector< TTi > & GetTiList()

Build ID set for this negative list.

void AddTi(TTi ti)

Add a new TI to the list.

int GetNumTis() const

Get the number of TIs in the array.

bool NotEmpty() const

Return true if there are elements present.

void AddIncludedOid(int oid)

Include an OID in the iteration.

void SetSiList(const vector< string > &new_list)

CSeqDBNegativeList(const CSeqDBNegativeList &other)

Prevent copy constructor.

void ReserveTis(size_t n)

Reserve space for TIs.

void SetPigList(const vector< TPig > &new_list)

void AddVisibleOid(int oid)

Indicate a visible OID.

bool GetOidStatus(int oid)

Get the inclusion status of an OID.

vector< TTi > m_Tis

TIs to exclude from the SeqDB instance.

TGi GetGi(int index) const

Access an element of the GI array.

vector< string > m_Sis

SeqIds to exclude from the SeqDB instance.

CSeqDBBitVector m_Visible

OIDs visible to the ISAM file.

vector< blastdb::TOid > m_ExcludedOids

int GetNumGis() const

Get the number of GIs in the array.

const vector< TGi > & GetGiList()

Build ID set for this negative list.

SBlastSeqIdListInfo m_ListInfo

const vector< blastdb::TOid > & GetExcludedOids()

CSeqDBNegativeList & operator=(const CSeqDBNegativeList &other)

Prevent assignment.

TTi GetTi(int index) const

Access an element of the TI array.

const vector< TPig > & GetPigList()

const string GetSi(int index) const

Access an element of the SeqId array.

void SetListInfo(const SBlastSeqIdListInfo &list_info)

vector< blastdb::TOid > & SetExcludedOids()

bool HasIdFilters() const

size_t m_LastSortSize

Zero if unsorted, or the size it had after the last sort.

vector< TGi > m_Gis

GIs to exclude from the SeqDB instance.

int Size(void)

Get list size.

int GetNumSis() const

Get the number of SeqIds in the array.

void ReserveSis(size_t n)

set< TTaxId > & GetTaxIdsList()

int GetNumOids()

Get the size of the OID array.

bool Empty() const

Return false if there are elements present.

const SBlastSeqIdListInfo & GetListInfo() const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static const char si[8][64]

std::ofstream out("events_result.xml")

main entry point for tests

bool Empty(const CNcbiOstrstream &src)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

EErrCode

Error types that an application can generate.

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJREAD_EXPORT

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

Front end for a platform-specific configuration summary.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

bool SeqDB_IsBinaryTiList(const string &fname)

Returns true if the file name passed contains a binary TI list.

USING_SCOPE(objects)

Include definitions from the objects namespace.

ESeqDBAllocType

Certain methods have an "Alloc" version.

map< string, TSeqDBAliasFileVersions > TSeqDBAliasFileValues

Contents of all alias file are returned in this type of container.

void SeqDB_GetLMDBFileExtensions(bool db_is_protein, vector< string > &extn)

Retrieves file extensions for BLAST LMDB files.

ESeqDBIdType SeqDB_SimplifySeqid(CSeq_id &bestid, const string *acc, Int8 &num_id, string &str_id, bool &simpler)

Seq-id simplification.

const blastdb::TOid kSeqDBEntryNotFound

void SeqDB_ReadMemoryMixList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SGiOid > &gis, vector< CSeqDBGiList::STiOid > &tis, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order)

Read an ID list (mixed type) from an area of memory.

string GetBlastSeqIdString(const CSeq_id &seqid, bool version)

Return ID string as stored in lmdb.

void SeqDB_ReadBinaryGiList(const string &name, vector< TGi > &gis)

Read a binary-format GI list from a file.

void SeqDB_ReadMemorySiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order=0)

Read a text SeqID list from an area of memory.

void SeqDB_ReadMixList(const string &fname, vector< CSeqDBGiList::SGiOid > &gis, vector< CSeqDBGiList::STiOid > &tis, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order)

Read a text SeqId list from a file.

void SeqDB_ReadPigList(const string &fname, vector< CSeqDBGiList::SPigOid > &pigs, bool *in_order=0)

const string kSeqDBGroupAliasFileName

The name of the group alias file name expected at each directory For more documentation,...

void SeqDB_ReadGiList(const string &fname, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order=0)

Read a text or binary GI list from a file.

Int4 TOid

Ordinal ID in BLAST databases.

const int kSeqDBNuclNcbiNA8

Used to request ambiguities in Ncbi/NA8 format.

bool IsStringId(const CSeq_id &id)

Determine if id is srting id.

ESeqDBIdType SeqDB_SimplifyAccession(const string &acc, Int8 &num_id, string &str_id, bool &simpler)

String id simplification.

void SeqDB_ReadMemoryGiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order=0)

Read a text or binary GI list from an area of memory.

bool SeqDB_IsBinaryGiList(const string &fname)

Read a text or binary SeqId list from a file.

vector< TSeqDBAliasFileInstance > TSeqDBAliasFileVersions

Contents of all instances of a particular alias file pathname.

void SeqDB_ReadTiList(const string &fname, vector< CSeqDBGiList::STiOid > &tis, bool *in_order=0)

Read a text or binary TI list from a file.

unsigned SeqDB_SequenceHash(const char *sequence, int length)

Returns a path minus filename.

const int kSeqDBNuclBlastNA8

Used to request ambiguities in BLAST/NA8 format.

void SeqDB_ReadSiList(const string &fname, vector< CSeqDBGiList::SSiOid > &sis, bool *in_order, SBlastSeqIdListInfo &db_info)

Read a text SeqId list from a file.

void SeqDB_GetFileExtensions(bool db_is_protein, vector< string > &extensions, EBlastDbVersion dbver=eBDB_Version4)

Retrieves a list of all supported file extensions for BLAST databases.

const string SeqDB_GetOidMaskFileExt(bool db_is_protein, EOidMaskType t)

string SeqDB_ResolveDbPathForLinkoutDB(const string &filename)

Resolve a file path using SeqDB's path algorithms.

void SeqDB_CombineAndQuote(const vector< string > &dbs, string &dbname)

Combine and quote a list of database names.

EBlastDbVersion

BLAST database version.

ESeqDBIdType

Various identifier formats used in Id lookup.

@ eStringId

Each PIG identifier refers to exactly one protein sequence.

@ eTiId

Genomic ID is a relatively stable numeric identifier for sequences.

@ ePigId

Trace ID is a numeric identifier for Trace sequences.

@ eHashId

Some sequence sources uses string identifiers.

@ eOID

Lookup from sequence hash values to OIDs.

bool SeqDB_CompareVolume(const string &volpath1, const string &volpath2)

Compares two volume file names and determine the volume order.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

string SeqDB_ResolveDbPathNoExtension(const string &filename, char dbtype='-')

Resolve a file path using SeqDB's path algorithms.

void SeqDB_ReadMemoryTiList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::STiOid > &tis, bool *in_order=0)

Read a text or binary TI list from an area of memory.

void SeqDB_GetMetadataFileExtension(bool db_is_protein, string &extn)

void SeqDB_SplitQuoted(const string &dbname, vector< CTempString > &dbs, bool keep_quote=false)

Split a (possibly) quoted list of database names into pieces.

const blastdb::TOid kSeqDBEntryDuplicate

map< string, string > TSeqDBAliasFileInstance

Set of values found in one instance of one alias file.

void SeqDB_ReadMemoryPigList(const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SPigOid > &pigs, bool *in_order=0)

Structure that holds GI,OID pairs.

TGi gi

The GI or 0 if unknown.

int oid

The OID or -1 if unknown.

SGiOid(TGi gi_in=ZERO_GI, int oid_in=-1)

Constuct an SGiOid element from the given gi and oid.

TPig pig

The PIG or 0 if unknown.

int oid

The OID or -1 if unknown.

SPigOid(TPig pig_in=0, int oid_in=-1)

Constuct an SPigOid element from the given pig and oid.

Structure that holds Seq-id,OID pairs.

string si

The String-id or "" if unknown.

SSiOid(const string &si_in="", int oid_in=-1)

Constuct a SSiOid element from the given Seq-id and oid.

int oid

The OID or -1 if unknown.

vector< blastdb::TOid > oids

Structure that holds TI,OID pairs.

STiOid(TTi ti_in=0, int oid_in=-1)

Constuct an STiOid element from the given TI (trace ID, expressed as a number) and oid.

int oid

The OID or -1 if unknown.

TTi ti

The TI or 0 if unknown.

Blast DB v5 seqid list info.

string common_name

Common name, such as "noisy night monkey".

string blast_name

A simple category name, such as "birds".

string s_kingdom

A string of length 1 indicating the "Super Kingdom".

SSeqDBTaxInfo(TTaxId t=ZERO_TAX_ID)

Default constructor.

string scientific_name

Scientific name, such as "Aotus vociferans".

friend ostream & operator<<(ostream &out, const SSeqDBTaxInfo &rhs)

TTaxId taxid

An identifier for this species or taxonomic group.

@ eTaxIdList

Filter a BLAST database via Taxonomy Id list.

@ eGiList

Filter a BLAST database via GIs.

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