Search Toolkit Book for CBlastServices
API for Remote Blast Services. More...
#include <objtools/blast/services/blast_services.hpp>
Inheritance diagram for CBlastServices:
Collaboration diagram for CBlastServices:
Public Types | |
| typedef vector< CRef< objects::CSeq_id > > | TSeqIdVector |
| Defines a std::vector of CRef<CSeq_id> More... | |
| typedef vector< CRef< objects::CBioseq > > | TBioseqVector |
| Defines a std::vector of CRef<CBioseq> More... | |
| typedef vector< CRef< objects::CSeq_interval > > | TSeqIntervalVector |
| Defines a std::vector of CRef<CSeq_interval> More... | |
| typedef vector< CRef< objects::CSeq_data > > | TSeqDataVector |
| Defines a std::vector of CRef<CSeq_data> 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... | |
Public Member Functions | |
| CBlastServices () | |
| Default constructor. More... | |
| void | SetVerbose (bool value=true) |
| Analogous to CRemoteBlast::SetVerbose. More... | |
| bool | IsValidBlastDb (const string &dbname, bool is_protein) |
| Returns true if the BLAST database specified exists in the NCBI servers. More... | |
| CRef< objects::CBlast4_database_info > | GetDatabaseInfo (CRef< objects::CBlast4_database > blastdb) |
| Retrieve detailed information for one BLAST database If information about multiple databases is needed, use the other GetDatabaseInfo method. More... | |
| vector< CRef< objects::CBlast4_database_info > > | GetDatabaseInfo (const string &dbname, bool is_protein, bool *found_all, vector< string > *missing_names=NULL) |
| Retrieve detailed information for databases listed in the string. More... | |
| vector< CRef< objects::CBlast4_database_info > > | GetDatabaseInfoLegacy (const string &dbname, bool is_protein, bool *found_all, vector< string > *missing_names=NULL) |
| Same as GetDatabaseInfo but retrieving whole list of database. More... | |
| vector< CRef< objects::CBlast4_database_info > > | GetOrganismSpecificRepeatsDatabases () |
| Retrieve organism specific repeats databases. More... | |
| objects::CBlast4_get_windowmasked_taxids_reply::Tdata | GetTaxIdWithWindowMaskerSupport () |
| Retrieve a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support an alternative organism specific filtering. 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... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. 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 |
Static Public Member Functions | |
| static void | GetSequencesInfo (TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false) |
| Get a set of Bioseqs without their sequence data given an input set of. More... | |
| static void | GetSequences (TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false) |
| Get a set of Bioseqs given an input set of Seq-ids. More... | |
| static void | GetSequenceParts (const TSeqIntervalVector &seqids, const string &database, char seqtype, TSeqIdVector &ids, TSeqDataVector &seq_data, string &errors, string &warnings, bool verbose=false) |
| This retrieves (partial) sequence data from the remote BLAST server. 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) |
Private Member Functions | |
| void | x_GetAvailableDatabases () |
| Retrieve the BLAST databases available for searching. More... | |
| CRef< objects::CBlast4_database_info > | x_FindDbInfoFromAvailableDatabases (CRef< objects::CBlast4_database > blastdb) |
| Look for a database matching this method's argument and returned detailed information about it. More... | |
| CBlastServices (const CBlastServices &) | |
| Prohibit copy construction. More... | |
| CBlastServices & | operator= (const CBlastServices &) |
| Prohibit assignment. More... | |
Private Attributes | |
| objects::CBlast4_get_databases_reply::Tdata | m_AvailableDatabases |
| BLAST databases available to search. More... | |
| objects::CBlast4_get_windowmasked_taxids_reply::Tdata | m_WindowMaskedTaxIds |
| Taxonomy IDs for which there's windowmasker masking data at NCBI. More... | |
| bool | m_Verbose |
| Display verbose output to stdout? More... | |
Additional Inherited Members | |
| 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 CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
API for Remote Blast Services.
Class to obtain information and data from the Remote BLAST service that is not associated with a specific BLAST search
Definition at line 106 of file blast_services.hpp.
The documentation for this class was generated from the following files:
- include/objtools/blast/services/blast_services.hpp
- src/objtools/blast/services/blast_services.cpp
