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NCBI C++ ToolKit: src/algo/blast/api/uniform_search.cpp Source File

: m_DbName(

), m_MolType(mol_type), m_GiListSet(

),

m_NeedsFilteringTranslation(

), m_DbInitialized(

)

& entrez_query)

: m_DbName(

), m_MolType(mol_type),

m_EntrezQueryLimitation(entrez_query), m_GiListSet(

),

m_NeedsFilteringTranslation(

), m_DbInitialized(

)

);

);

(vector<string>, iter, sis) {

seqIds->

(*iter);

vector<TPig> pig_list;

vector<int> supported_algorithms;

(find(supported_algorithms.begin(),

supported_algorithms.end(),

<<

<<

(

() ?

:

) <<

ESubjectMaskingType

Define the possible subject masking types.

Defines BLAST error codes (user errors included)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

int GetNumGis() const

Get the number of GIs in the array.

int GetNumSis() const

Get the number of Seq-ids in the array.

void GetPigList(vector< TPig > &pigs) const

void GetGiList(vector< TGi > &gis) const

Get the gi list.

void GetSiList(vector< string > &sis) const

TODO Get the seqid list?

const SBlastSeqIdListInfo & GetListInfo()

set< TTaxId > & GetTaxIdsList()

bool Empty() const

Return false if there are elements present.

SeqDB ID list for performing boolean set operations.

void AddTaxIds(const set< TTaxId > &tax_ids)

void AddSi(const string &si)

Add a new SeqId to the list.

void SetPigList(const vector< TPig > &new_list)

void SetListInfo(const SBlastSeqIdListInfo &list_info)

void ReserveSis(size_t n)

void GetAvailableMaskAlgorithms(vector< int > &algorithms)

Get a list of algorithm IDs for which mask data exists.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

int GetMaskAlgorithmId(const string &algo_name) const

Get the numeric algorithm ID for a string.

void SetEntrezQueryLimitation(const string &entrez_query)

Mutator for the entrez query.

string GetDatabaseName() const

Accessor for the database name.

int m_FilteringAlgorithmId

void SetMoleculeType(EMoleculeType mol_type)

Mutator for the molecule type.

bool m_NeedsFilteringTranslation

void SetNegativeGiList(CSeqDBGiList *gilist)

Mutator for the negative gi list.

EMoleculeType GetMoleculeType() const

Accessor for the molecule type.

string m_EntrezQueryLimitation

entrez query

string m_FilteringAlgorithmString

filtering to apply to database sequences

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

const TGiList GetNegativeGiListLimitation() const

CRef< CSeqDBGiList > m_GiList

gi list

const CRef< CSeqDBGiList > & GetNegativeGiList() const

Accessor for the negative gi list.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

string GetFilteringAlgorithmKey() const

Accessor for the filtering algorithm key.

bool IsProtein() const

Determine whether this database contains protein sequences or not.

void x_TranslateFilteringAlgorithm() const

Translate string algorithm id to numeric id.

void SetDatabaseName(const string &dbname)

Mutator for the database name.

string m_DbName

database name

EMoleculeType m_MolType

molecule type

vector< TGi > TGiList

Define a list of gis.

static bool s_IsNumericId(const string &id)

CRef< CSeqDBGiList > m_NegativeGiList

negative gi list

ESubjectMaskingType m_MaskType

ESubjectMaskingType GetMaskType() const

void x_InitializeDb() const

Initialize the database.

void SetSeqDb(CRef< CSeqDB > seqdb)

Mutator for the seqdb.

const CRef< CSeqDBGiList > & GetGiList() const

Accessor for the gi list.

const TGiList GetGiListLimitation() const

CSearchDatabase(const string &dbname, EMoleculeType mol_type)

Simple constructor.

void x_ValidateMaskingAlgorithm() const

Validates that the specified filtering algorithm ID is supported by the specified BLAST database.

void SetFilteringAlgorithm(int filt_algorithm_id)

Temporary fix for backwards compatibility with other 6.0 SCs.

EMoleculeType

Molecule of the BLAST database.

string GetEntrezQueryLimitation() const

Accessor for the entrez query.

void SetGiList(CSeqDBGiList *gilist)

Mutator for the gi list.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

@ fConvErr_NoThrow

Do not throw an exception on error.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Uniform BLAST Search Interface.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

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