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Search Toolkit Book for CBl2Seq

Runs the BLAST algorithm between 2 sequences. More...

#include <algo/blast/api/bl2seq.hpp>

+ Inheritance diagram for CBl2Seq:
+ Collaboration diagram for CBl2Seq:

Public Member Functions

 CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
 Constructor to compare 2 sequences with default options. More...
 
 CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
 Constructor to compare query against all subject sequences with default options. More...
 
 CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
 Constructor to allow query concatenation with default options. More...
 
 CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)
 Constructor to compare 2 sequences with specified options. More...
 
 CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
 Constructor to compare query against all subject sequences with specified options. More...
 
 CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
 Constructor to allow query concatenation with specified options. More...
 
virtual ~CBl2Seq ()
 Destructor. More...
 
void SetQuery (const SSeqLoc &query)
 Set the query. More...
 
const SSeqLocGetQuery () const
 Retrieve the query sequence. More...
 
void SetQueries (const TSeqLocVector &queries)
 Set a vector of query sequences for a concatenated search. More...
 
const TSeqLocVectorGetQueries () const
 Retrieve a vector of query sequences. More...
 
void SetSubject (const SSeqLoc &subject)
 Set the subject sequence. More...
 
const SSeqLocGetSubject () const
 Retrieve the subject sequence. More...
 
void SetSubjects (const TSeqLocVector &subjects)
 Set a vector of subject sequences. More...
 
const TSeqLocVectorGetSubjects () const
 Retrieve a vector of subject sequences. More...
 
CBlastOptionsHandleSetOptionsHandle ()
 Set the options handle. More...
 
const CBlastOptionsHandleGetOptionsHandle () const
 Retrieve the options handle. More...
 
virtual TSeqAlignVector Run ()
 Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, ... More...
 
CRef< CSearchResultSetRunEx ()
 Performs the same functionality as Run(), but it returns a different data type. More...
 
TSeqLocInfoVector GetFilteredQueryRegions () const
 Retrieves regions filtered on the query/queries. More...
 
void GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const
 Retrieves regions filtered on the subject sequence(s) More...
 
BlastDiagnosticsGetDiagnostics () const
 Retrieves the diagnostics information returned from the engine. More...
 
void GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
 Get the ancillary results for a BLAST search (to be used with the Run() method) More...
 
void GetMessages (TSearchMessages &messages) const
 Returns error messages/warnings. More...
 
TInterruptFnPtr SetInterruptCallback (TInterruptFnPtr fnptr, void *user_data=NULL)
 Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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 TSeqAlignVector CSearchResultSet2TSeqAlignVector (CRef< CSearchResultSet > res)
 Converts m_Results data member to a TSeqAlignVector. 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)
 

Protected Member Functions

void x_BuildAncillaryData ()
 Populate the internal m_AncillaryData member. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Member Functions

void x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
 Common initialization code for all c-tors. More...
 
void x_InitCLocalBlast ()
 Common initialization of the CLocalBlast object. More...
 
 CBl2Seq (const CBl2Seq &rhs)
 Prohibit copy constructor. More...
 
CBl2Seqoperator= (const CBl2Seq &rhs)
 Prohibit assignment operator. More...
 
void x_ResetInternalDs ()
 Clean up structures and results from any previous search. More...
 

Private Attributes

TSeqLocVector m_tQueries
 query sequence(s) More...
 
TSeqLocVector m_tSubjects
 sequence(s) to BLAST against More...
 
CRef< CBlastOptionsHandlem_OptsHandle
 Blast options. More...
 
CRef< CLocalBlastm_Blast
 The actual BLAST instance. More...
 
bool m_DbScanMode
 Scan like a databsase (as opposed to pairwise) More...
 
TSearchMessages m_Messages
 Stores any warnings emitted during query setup. More...
 
BlastDiagnosticsmi_pDiagnostics
 Return search statistics data. More...
 
CSearchResultSet::TAncillaryVector m_AncillaryData
 Ancillary BLAST data. More...
 
CRef< CSearchResultSetm_Results
 CLocalBlast results. More...
 
TInterruptFnPtr m_InterruptFnx
 Interrupt callback. More...
 
void * m_InterruptUserData
 Interrupt user datacallback. More...
 

Friends

class ::CBlastFilterTest
 

Additional Inherited Members

- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. 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...
 

Detailed Description

Runs the BLAST algorithm between 2 sequences.

Note
this is a single-BLAST search run object (i.e.: it caches the results after a BLAST search is done). If multiple BLAST searches with different queries, subjects, or options are required, please create a separate object

Definition at line 57 of file bl2seq.hpp.


The documentation for this class was generated from the following files:
Modified on Wed May 22 11:27:41 2024 by modify_doxy.py rev. 669887