NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members

Search Toolkit Book for CIgBlast

#include <algo/blast/igblast/igblast.hpp>

+ Inheritance diagram for CIgBlast:
+ Collaboration diagram for CIgBlast:

Public Member Functions

 CIgBlast (CRef< CBlastQueryVector > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, CRef< CScope > scope)
 Local Igblast search API. More...
 
 CIgBlast (CRef< CBlastQueryVector > query_factory, CRef< CSearchDatabase > blastdb, CRef< IQueryFactory > subjects, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, string entrez_query, CRef< CScope > scope)
 Remote Igblast search API. More...
 
 ~CIgBlast ()
 Destructor. More...
 
CRef< CSearchResultSetRun ()
 Run the Ig-BLAST engine. More...
 
void SetNumberOfThreads (size_t nthreads)
 Set MT mode. More...
 
string GetRid ()
 
- 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
 

Private Member Functions

 CIgBlast (const CIgBlast &rhs)
 Prohibit copy constructor. More...
 
CIgBlastoperator= (const CIgBlast &rhs)
 Prohibit assignment operator. More...
 
void x_SetupVSearch (CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)
 Prepare blast option handle and query for V germline database search. More...
 
void x_SetupDJSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)
 Prepare blast option handle and query for D, J germline database search. More...
 
void x_SetupCRegionSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)
 
void x_SetupNoOverlapDSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< CSearchResultSet > &results, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)
 
void x_SetupDbSearch (vector< CRef< CIgAnnotation > > &annot, CRef< IQueryFactory > &qf)
 Prepare blast option handle and query for specified database search. More...
 
void x_AnnotateV (CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)
 Annotate the V gene based on blast results. More...
 
void x_AnnotateDJ (CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)
 Annotate the D and J genes based on blast results. More...
 
void x_AnnotateD (CRef< CSearchResultSet > &results_D, vector< CRef< CIgAnnotation > > &annot)
 
void x_AnnotateJ (CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)
 
void x_AnnotateC (CRef< CSearchResultSet > &results_c, CRef< CSearchResultSet > &results_j, vector< CRef< CIgAnnotation > > &annot)
 
void x_AnnotateDomain (CRef< CSearchResultSet > &gl_results, CRef< CSearchResultSet > &dm_results, vector< CRef< CIgAnnotation > > &annot)
 Annotate the query chaintype and domains based on blast results. More...
 
void x_SetChainType (CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)
 Set the subject chain type and frame info. More...
 
void x_ConvertResultType (CRef< CSearchResultSet > &results)
 Convert bl2seq result to database search mode. More...
 
void x_SetAnnotation (vector< CRef< CIgAnnotation > > &annot, CRef< CSearchResultSet > &final_results)
 Append annotation info to the final results. More...
 
void x_FindDJ (CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, CRef< CIgAnnotation > &annot, CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq)
 
void x_FindDJAln (CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq, bool va_or_vd_as_heavy_chain)
 
void x_ExtendAlign5end (CRef< CSearchResultSet > &results)
 
void x_ExtendAlign3end (CRef< CSearchResultSet > &results)
 
void x_ScreenByAlignLength (CRef< CSearchResultSet > &results, int length)
 
void x_FillJDomain (CRef< CSeq_align > &align, CRef< CIgAnnotation > &annot)
 
void x_ProcessDJResult (CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)
 
void x_ProcessDGeneResult (CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)
 
void x_ProcessCResult (CRef< CSearchResultSet > &results_C, vector< CRef< CIgAnnotation > > &annots)
 

Static Private Member Functions

static void s_SortResultsByEvalue (CRef< CSearchResultSet > &results)
 Sort blast results according to evalue. More...
 
static void s_AppendResults (CRef< CSearchResultSet > &results, int num_aligns, int gene, CRef< CSearchResultSet > &final_results)
 Append blast results to the final results. More...
 

Private Attributes

bool m_IsLocal
 
size_t m_NumThreads
 
CRef< CBlastQueryVectorm_Query
 
CRef< IQueryFactorym_Subject
 
CRef< CLocalDbAdapterm_LocalDb
 
CRef< CSearchDatabasem_RemoteDb
 
CRef< CBlastOptionsHandlem_Options
 
CConstRef< CIgBlastOptionsm_IgOptions
 
CIgAnnotationInfo m_AnnotationInfo
 
string m_EntrezQuery
 
CRef< CScopem_Scope
 
string m_RID
 

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 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)
 
- 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

Definition at line 236 of file igblast.hpp.


The documentation for this class was generated from the following files:
Modified on Sat Dec 02 09:21:16 2023 by modify_doxy.py rev. 669887