Search Toolkit Book for CPssmWithParameters
#include <objects/scoremat/PssmWithParameters.hpp>
Inheritance diagram for CPssmWithParameters:
Collaboration diagram for CPssmWithParameters:
Public Member Functions | |
| CPssmWithParameters (void) | |
| ~CPssmWithParameters (void) | |
| bool | HasQuery () const |
| Has this PSSM a query in it? More... | |
| const CSeq_entry & | GetQuery () const |
| Retrieve the query sequence. More... | |
| CSeq_entry & | SetQuery () |
| Retrieve the query sequence. More... | |
| Public Member Functions inherited from CPssmWithParameters_Base | |
| CPssmWithParameters_Base (void) | |
| virtual | ~CPssmWithParameters_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetPssm (void) const |
| This field is applicable to PSI-BLAST and formatrpsdb. More... | |
| bool | CanGetPssm (void) const |
| Check if it is safe to call GetPssm method. More... | |
| void | ResetPssm (void) |
| Reset Pssm data member. More... | |
| const TPssm & | GetPssm (void) const |
| Get the Pssm member data. More... | |
| void | SetPssm (TPssm &value) |
| Assign a value to Pssm data member. More... | |
| TPssm & | SetPssm (void) |
| Assign a value to Pssm data member. More... | |
| bool | IsSetParams (void) const |
| This field's rpsdbparams is used to specify the values of options for processing by formatrpsdb. More... | |
| bool | CanGetParams (void) const |
| Check if it is safe to call GetParams method. More... | |
| void | ResetParams (void) |
| Reset Params data member. More... | |
| const TParams & | GetParams (void) const |
| Get the Params member data. More... | |
| void | SetParams (TParams &value) |
| Assign a value to Params data member. More... | |
| TParams & | SetParams (void) |
| Assign a value to Params data member. More... | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More... | |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. 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... | |
| 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 Types | |
| typedef CPssmWithParameters_Base | Tparent |
Private Member Functions | |
| CPssmWithParameters (const CPssmWithParameters &value) | |
| CPssmWithParameters & | operator= (const CPssmWithParameters &value) |
Additional Inherited Members | |
| Public Types inherited from CPssmWithParameters_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_pssm , e_params } |
| typedef CPssm | TPssm |
| typedef CPssmParameters | TParams |
| typedef Tparent::CMemberIndex< E_memberIndex, 3 > | TmemberIndex |
| 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... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| 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 CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| 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 55 of file PssmWithParameters.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 57 of file PssmWithParameters.hpp.
Constructor & Destructor Documentation
◆ CPssmWithParameters() [1/2]
|
inline |
Definition at line 82 of file PssmWithParameters.hpp.
◆ ~CPssmWithParameters()
| CPssmWithParameters::~CPssmWithParameters | ( | void | ) |
Definition at line 50 of file PssmWithParameters.cpp.
◆ CPssmWithParameters() [2/2]
|
private |
Member Function Documentation
◆ GetQuery()
| const CSeq_entry & CPssmWithParameters::GetQuery | ( | void | ) | const |
Retrieve the query sequence.
Definition at line 61 of file PssmWithParameters.cpp.
References CPssmWithParameters_Base::GetPssm(), and CPssm_Base::GetQuery().
Referenced by BOOST_AUTO_TEST_CASE(), CTblastnNode::Main(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CVDBTblastnApp::Run(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CRemoteBlast::x_ExtractQueryIds(), and CTblastnApp::x_RunMTBySplitDB().
◆ HasQuery()
| bool CPssmWithParameters::HasQuery | ( | ) | const |
Has this PSSM a query in it?
Definition at line 55 of file PssmWithParameters.cpp.
References CPssmWithParameters_Base::CanGetPssm(), and CPssmWithParameters_Base::GetPssm().
Referenced by BOOST_AUTO_TEST_CASE(), CTblastnNode::Main(), CPsiBlastApp::Run(), CVDBTblastnApp::Run(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), and CTblastnApp::x_RunMTBySplitDB().
◆ operator=()
|
private |
◆ SetQuery()
| CSeq_entry & CPssmWithParameters::SetQuery | ( | void | ) |
Retrieve the query sequence.
Definition at line 67 of file PssmWithParameters.cpp.
References CPssmWithParameters_Base::SetPssm(), and CPssm_Base::SetQuery().
Referenced by CTblastnNode::Main(), CPsiBlastApp::Run(), CVDBTblastnApp::Run(), s_AddSeqDataToPssm(), s_AddSeqTitleToPssm(), s_GetQueryBioseq(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), and CTblastnApp::x_RunMTBySplitDB().
The documentation for this class was generated from the following files:
- include/objects/scoremat/PssmWithParameters.hpp
- src/objects/scoremat/PssmWithParameters.cpp
