Search Toolkit Book for CPssmFinalData_Base
=========================================================================== PSI-BLAST, formatrpsdb, RPS-BLAST workflow: =========================================== More...
#include <objects/scoremat/PssmFinalData_.hpp>
Inheritance diagram for CPssmFinalData_Base:
Collaboration diagram for CPssmFinalData_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_scores , e_lambda , e_kappa , e_h , e_scalingFactor , e_lambdaUngapped , e_kappaUngapped , e_hUngapped , e_wordScoreThreshold } |
| typedef list< int > | TScores |
| typedef double | TLambda |
| typedef double | TKappa |
| typedef double | TH |
| typedef int | TScalingFactor |
| typedef double | TLambdaUngapped |
| typedef double | TKappaUngapped |
| typedef double | THUngapped |
| typedef double | TWordScoreThreshold |
| typedef Tparent::CMemberIndex< E_memberIndex, 10 > | 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... | |
Public Member Functions | |
| CPssmFinalData_Base (void) | |
| virtual | ~CPssmFinalData_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetScores (void) const |
| PSSM's scores Check if a value has been assigned to Scores data member. More... | |
| bool | CanGetScores (void) const |
| Check if it is safe to call GetScores method. More... | |
| void | ResetScores (void) |
| Reset Scores data member. More... | |
| const TScores & | GetScores (void) const |
| Get the Scores member data. More... | |
| TScores & | SetScores (void) |
| Assign a value to Scores data member. More... | |
| bool | IsSetLambda (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to Lambda data member. More... | |
| bool | CanGetLambda (void) const |
| Check if it is safe to call GetLambda method. More... | |
| void | ResetLambda (void) |
| Reset Lambda data member. More... | |
| TLambda | GetLambda (void) const |
| Get the Lambda member data. More... | |
| void | SetLambda (TLambda value) |
| Assign a value to Lambda data member. More... | |
| TLambda & | SetLambda (void) |
| Assign a value to Lambda data member. More... | |
| bool | IsSetKappa (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to Kappa data member. More... | |
| bool | CanGetKappa (void) const |
| Check if it is safe to call GetKappa method. More... | |
| void | ResetKappa (void) |
| Reset Kappa data member. More... | |
| TKappa | GetKappa (void) const |
| Get the Kappa member data. More... | |
| void | SetKappa (TKappa value) |
| Assign a value to Kappa data member. More... | |
| TKappa & | SetKappa (void) |
| Assign a value to Kappa data member. More... | |
| bool | IsSetH (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to H data member. More... | |
| bool | CanGetH (void) const |
| Check if it is safe to call GetH method. More... | |
| void | ResetH (void) |
| Reset H data member. More... | |
| TH | GetH (void) const |
| Get the H member data. More... | |
| void | SetH (TH value) |
| Assign a value to H data member. More... | |
| TH & | SetH (void) |
| Assign a value to H data member. More... | |
| bool | IsSetScalingFactor (void) const |
| scaling factor used to obtain more precision when building the PSSM. More... | |
| bool | CanGetScalingFactor (void) const |
| Check if it is safe to call GetScalingFactor method. More... | |
| void | ResetScalingFactor (void) |
| Reset ScalingFactor data member. More... | |
| void | SetDefaultScalingFactor (void) |
| Assign default value to ScalingFactor data member. More... | |
| TScalingFactor | GetScalingFactor (void) const |
| Get the ScalingFactor member data. More... | |
| void | SetScalingFactor (TScalingFactor value) |
| Assign a value to ScalingFactor data member. More... | |
| TScalingFactor & | SetScalingFactor (void) |
| Assign a value to ScalingFactor data member. More... | |
| bool | IsSetLambdaUngapped (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to LambdaUngapped data member. More... | |
| bool | CanGetLambdaUngapped (void) const |
| Check if it is safe to call GetLambdaUngapped method. More... | |
| void | ResetLambdaUngapped (void) |
| Reset LambdaUngapped data member. More... | |
| TLambdaUngapped | GetLambdaUngapped (void) const |
| Get the LambdaUngapped member data. More... | |
| void | SetLambdaUngapped (TLambdaUngapped value) |
| Assign a value to LambdaUngapped data member. More... | |
| TLambdaUngapped & | SetLambdaUngapped (void) |
| Assign a value to LambdaUngapped data member. More... | |
| bool | IsSetKappaUngapped (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to KappaUngapped data member. More... | |
| bool | CanGetKappaUngapped (void) const |
| Check if it is safe to call GetKappaUngapped method. More... | |
| void | ResetKappaUngapped (void) |
| Reset KappaUngapped data member. More... | |
| TKappaUngapped | GetKappaUngapped (void) const |
| Get the KappaUngapped member data. More... | |
| void | SetKappaUngapped (TKappaUngapped value) |
| Assign a value to KappaUngapped data member. More... | |
| TKappaUngapped & | SetKappaUngapped (void) |
| Assign a value to KappaUngapped data member. More... | |
| bool | IsSetHUngapped (void) const |
| Karlin & Altschul parameter produced during the PSSM's calculation Check if a value has been assigned to HUngapped data member. More... | |
| bool | CanGetHUngapped (void) const |
| Check if it is safe to call GetHUngapped method. More... | |
| void | ResetHUngapped (void) |
| Reset HUngapped data member. More... | |
| THUngapped | GetHUngapped (void) const |
| Get the HUngapped member data. More... | |
| void | SetHUngapped (THUngapped value) |
| Assign a value to HUngapped data member. More... | |
| THUngapped & | SetHUngapped (void) |
| Assign a value to HUngapped data member. More... | |
| bool | IsSetWordScoreThreshold (void) const |
| Word score threshold Check if a value has been assigned to WordScoreThreshold data member. More... | |
| bool | CanGetWordScoreThreshold (void) const |
| Check if it is safe to call GetWordScoreThreshold method. More... | |
| void | ResetWordScoreThreshold (void) |
| Reset WordScoreThreshold data member. More... | |
| TWordScoreThreshold | GetWordScoreThreshold (void) const |
| Get the WordScoreThreshold member data. More... | |
| void | SetWordScoreThreshold (TWordScoreThreshold value) |
| Assign a value to WordScoreThreshold data member. More... | |
| TWordScoreThreshold & | SetWordScoreThreshold (void) |
| Assign a value to WordScoreThreshold 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 CSerialObject | Tparent |
Private Member Functions | |
| CPssmFinalData_Base (const CPssmFinalData_Base &) | |
| CPssmFinalData_Base & | operator= (const CPssmFinalData_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| list< int > | m_Scores |
| double | m_Lambda |
| double | m_Kappa |
| double | m_H |
| int | m_ScalingFactor |
| double | m_LambdaUngapped |
| double | m_KappaUngapped |
| double | m_HUngapped |
| double | m_WordScoreThreshold |
Additional Inherited Members | |
| 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
=========================================================================== PSI-BLAST, formatrpsdb, RPS-BLAST workflow: ===========================================
Two possible inputs to PSI-BLAST and formatrpsdb: 1) PssmWithParams where pssm field contains intermediate PSSM data (matrix of frequency ratios) 2) PssmWithParams where pssm field contains final PSSM data (matrix of scores and statistical parameters) - such as written by cddumper
In case 1, PSI-BLAST's PSSM engine is invoked to create the PSSM and perform the PSI-BLAST search or build the PSSM to then build the RPS-BLAST database. In case 2, PSI-BLAST's PSSM engine is not invoked and the matrix of scores statistical parameters are used to perform the search in PSI-BLAST and the same data and the data in PssmWithParams::params::rpsdbparams is used to build the PSSM and ultimately the RPS-BLAST database
reads ++++++++++++++ writes PssmWithParams ====> + PSI-BLAST + =====> PssmWithParams ++++++++++++++ | ^ ^ | | | | | +===========================================+ | | | +===========================================+ | | | reads | | v | +++++++++++++++ writes +++++++++++++++++++++++ | | formatrpsdb | =====> | RPS-BLAST databases | | +++++++++++++++ +++++++++++++++++++++++ | ^ | | | | reads | +++++++++++++ | | RPS-BLAST | | +++++++++++++ | | reads ++++++++++++ writes | Cdd ======> | cddumper | =============================+ ++++++++++++
=========================================================================== Contains the PSSM's scores and its associated statistical parameters. Dimensions and order in which scores are stored must be the same as that specified in Pssm::numRows, Pssm::numColumns, and Pssm::byrow
Definition at line 119 of file PssmFinalData_.hpp.
The documentation for this class was generated from the following files:
- include/objects/scoremat/PssmFinalData_.hpp
- src/objects/scoremat/PssmFinalData_.cpp
