Search Toolkit Book for CPssmParameters
#include <objects/scoremat/PssmParameters.hpp>
Inheritance diagram for CPssmParameters:
Collaboration diagram for CPssmParameters:
Public Member Functions | |
| CPssmParameters (void) | |
| ~CPssmParameters (void) | |
| Public Member Functions inherited from CPssmParameters_Base | |
| CPssmParameters_Base (void) | |
| virtual | ~CPssmParameters_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetPseudocount (void) const |
| pseudocount constant used for PSSM. More... | |
| bool | CanGetPseudocount (void) const |
| Check if it is safe to call GetPseudocount method. More... | |
| void | ResetPseudocount (void) |
| Reset Pseudocount data member. More... | |
| TPseudocount | GetPseudocount (void) const |
| Get the Pseudocount member data. More... | |
| void | SetPseudocount (TPseudocount value) |
| Assign a value to Pseudocount data member. More... | |
| TPseudocount & | SetPseudocount (void) |
| Assign a value to Pseudocount data member. More... | |
| bool | IsSetRpsdbparams (void) const |
| data needed by formatrpsdb to create RPS-BLAST databases. More... | |
| bool | CanGetRpsdbparams (void) const |
| Check if it is safe to call GetRpsdbparams method. More... | |
| void | ResetRpsdbparams (void) |
| Reset Rpsdbparams data member. More... | |
| const TRpsdbparams & | GetRpsdbparams (void) const |
| Get the Rpsdbparams member data. More... | |
| void | SetRpsdbparams (TRpsdbparams &value) |
| Assign a value to Rpsdbparams data member. More... | |
| TRpsdbparams & | SetRpsdbparams (void) |
| Assign a value to Rpsdbparams data member. More... | |
| bool | IsSetConstraints (void) const |
| alignment constraints needed by sequence-structure threader and other global or local block-alignment algorithms Check if a value has been assigned to Constraints data member. More... | |
| bool | CanGetConstraints (void) const |
| Check if it is safe to call GetConstraints method. More... | |
| void | ResetConstraints (void) |
| Reset Constraints data member. More... | |
| const TConstraints & | GetConstraints (void) const |
| Get the Constraints member data. More... | |
| void | SetConstraints (TConstraints &value) |
| Assign a value to Constraints data member. More... | |
| TConstraints & | SetConstraints (void) |
| Assign a value to Constraints data member. More... | |
| bool | IsSetBitScoreThresh (void) const |
| bit score threshold for specific conserved domain hits Check if a value has been assigned to BitScoreThresh data member. More... | |
| bool | CanGetBitScoreThresh (void) const |
| Check if it is safe to call GetBitScoreThresh method. More... | |
| void | ResetBitScoreThresh (void) |
| Reset BitScoreThresh data member. More... | |
| TBitScoreThresh | GetBitScoreThresh (void) const |
| Get the BitScoreThresh member data. More... | |
| void | SetBitScoreThresh (TBitScoreThresh value) |
| Assign a value to BitScoreThresh data member. More... | |
| TBitScoreThresh & | SetBitScoreThresh (void) |
| Assign a value to BitScoreThresh data member. More... | |
| bool | IsSetBitScoreReportingThresh (void) const |
| bit score threshold for reporting any conserved domain hits Check if a value has been assigned to BitScoreReportingThresh data member. More... | |
| bool | CanGetBitScoreReportingThresh (void) const |
| Check if it is safe to call GetBitScoreReportingThresh method. More... | |
| void | ResetBitScoreReportingThresh (void) |
| Reset BitScoreReportingThresh data member. More... | |
| TBitScoreReportingThresh | GetBitScoreReportingThresh (void) const |
| Get the BitScoreReportingThresh member data. More... | |
| void | SetBitScoreReportingThresh (TBitScoreReportingThresh value) |
| Assign a value to BitScoreReportingThresh data member. More... | |
| TBitScoreReportingThresh & | SetBitScoreReportingThresh (void) |
| Assign a value to BitScoreReportingThresh data member. More... | |
| bool | IsSetAnnotatedSites (void) const |
| conserved functional sites with annotations Check if a value has been assigned to AnnotatedSites data member. More... | |
| bool | CanGetAnnotatedSites (void) const |
| Check if it is safe to call GetAnnotatedSites method. More... | |
| void | ResetAnnotatedSites (void) |
| Reset AnnotatedSites data member. More... | |
| const TAnnotatedSites & | GetAnnotatedSites (void) const |
| Get the AnnotatedSites member data. More... | |
| void | SetAnnotatedSites (TAnnotatedSites &value) |
| Assign a value to AnnotatedSites data member. More... | |
| TAnnotatedSites & | SetAnnotatedSites (void) |
| Assign a value to AnnotatedSites 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 CPssmParameters_Base | Tparent |
Private Member Functions | |
| CPssmParameters (const CPssmParameters &value) | |
| CPssmParameters & | operator= (const CPssmParameters &value) |
Additional Inherited Members | |
| Public Types inherited from CPssmParameters_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_pseudocount , e_rpsdbparams , e_constraints , e_bitScoreThresh , e_bitScoreReportingThresh , e_annotatedSites } |
| typedef int | TPseudocount |
| typedef CFormatRpsDbParameters | TRpsdbparams |
| typedef CCoreDef | TConstraints |
| typedef double | TBitScoreThresh |
| typedef double | TBitScoreReportingThresh |
| typedef CSite_annot_set | TAnnotatedSites |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | 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 65 of file PssmParameters.hpp.
The documentation for this class was generated from the following files:
- include/objects/scoremat/PssmParameters.hpp
- src/objects/scoremat/PssmParameters.cpp
