Search Toolkit Book for CPssm_Base
Position-specific scoring matrix. More...
#include <objects/scoremat/Pssm_.hpp>
Inheritance diagram for CPssm_Base:
Collaboration diagram for CPssm_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_isProtein , e_identifier , e_numRows , e_numColumns , e_rowLabels , e_byRow , e_query , e_intermediateData , e_finalData } |
| typedef bool | TIsProtein |
| typedef CObject_id | TIdentifier |
| typedef int | TNumRows |
| typedef int | TNumColumns |
| typedef list< string > | TRowLabels |
| typedef bool | TByRow |
| typedef CSeq_entry | TQuery |
| typedef CPssmIntermediateData | TIntermediateData |
| typedef CPssmFinalData | TFinalData |
| 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 | |
| CPssm_Base (void) | |
| virtual | ~CPssm_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetIsProtein (void) const |
| Is the this a protein or nucleotide scoring matrix? Check if a value has been assigned to IsProtein data member. More... | |
| bool | CanGetIsProtein (void) const |
| Check if it is safe to call GetIsProtein method. More... | |
| void | ResetIsProtein (void) |
| Reset IsProtein data member. More... | |
| void | SetDefaultIsProtein (void) |
| Assign default value to IsProtein data member. More... | |
| TIsProtein | GetIsProtein (void) const |
| Get the IsProtein member data. More... | |
| void | SetIsProtein (TIsProtein value) |
| Assign a value to IsProtein data member. More... | |
| TIsProtein & | SetIsProtein (void) |
| Assign a value to IsProtein data member. More... | |
| bool | IsSetIdentifier (void) const |
| PSSM identifier Check if a value has been assigned to Identifier data member. More... | |
| bool | CanGetIdentifier (void) const |
| Check if it is safe to call GetIdentifier method. More... | |
| void | ResetIdentifier (void) |
| Reset Identifier data member. More... | |
| const TIdentifier & | GetIdentifier (void) const |
| Get the Identifier member data. More... | |
| void | SetIdentifier (TIdentifier &value) |
| Assign a value to Identifier data member. More... | |
| TIdentifier & | SetIdentifier (void) |
| Assign a value to Identifier data member. More... | |
| bool | IsSetNumRows (void) const |
| The dimensions of the matrix are returned so the client can verify that all data was received. More... | |
| bool | CanGetNumRows (void) const |
| Check if it is safe to call GetNumRows method. More... | |
| void | ResetNumRows (void) |
| Reset NumRows data member. More... | |
| TNumRows | GetNumRows (void) const |
| Get the NumRows member data. More... | |
| void | SetNumRows (TNumRows value) |
| Assign a value to NumRows data member. More... | |
| TNumRows & | SetNumRows (void) |
| Assign a value to NumRows data member. More... | |
| bool | IsSetNumColumns (void) const |
| number of columns Check if a value has been assigned to NumColumns data member. More... | |
| bool | CanGetNumColumns (void) const |
| Check if it is safe to call GetNumColumns method. More... | |
| void | ResetNumColumns (void) |
| Reset NumColumns data member. More... | |
| TNumColumns | GetNumColumns (void) const |
| Get the NumColumns member data. More... | |
| void | SetNumColumns (TNumColumns value) |
| Assign a value to NumColumns data member. More... | |
| TNumColumns & | SetNumColumns (void) |
| Assign a value to NumColumns data member. More... | |
| bool | IsSetRowLabels (void) const |
| row-labels is given to note the order of residue types so that it can be cross-checked between applications. More... | |
| bool | CanGetRowLabels (void) const |
| Check if it is safe to call GetRowLabels method. More... | |
| void | ResetRowLabels (void) |
| Reset RowLabels data member. More... | |
| const TRowLabels & | GetRowLabels (void) const |
| Get the RowLabels member data. More... | |
| TRowLabels & | SetRowLabels (void) |
| Assign a value to RowLabels data member. More... | |
| bool | IsSetByRow (void) const |
| are matrices stored row by row? Check if a value has been assigned to ByRow data member. More... | |
| bool | CanGetByRow (void) const |
| Check if it is safe to call GetByRow method. More... | |
| void | ResetByRow (void) |
| Reset ByRow data member. More... | |
| void | SetDefaultByRow (void) |
| Assign default value to ByRow data member. More... | |
| TByRow | GetByRow (void) const |
| Get the ByRow member data. More... | |
| void | SetByRow (TByRow value) |
| Assign a value to ByRow data member. More... | |
| TByRow & | SetByRow (void) |
| Assign a value to ByRow data member. More... | |
| bool | IsSetQuery (void) const |
| PSSM representative sequence (master) Check if a value has been assigned to Query data member. More... | |
| bool | CanGetQuery (void) const |
| Check if it is safe to call GetQuery method. More... | |
| void | ResetQuery (void) |
| Reset Query data member. More... | |
| const TQuery & | GetQuery (void) const |
| Get the Query member data. More... | |
| void | SetQuery (TQuery &value) |
| Assign a value to Query data member. More... | |
| TQuery & | SetQuery (void) |
| Assign a value to Query data member. More... | |
| bool | IsSetIntermediateData (void) const |
| both intermediateData and finalData can be provided, but at least one of them must be provided. More... | |
| bool | CanGetIntermediateData (void) const |
| Check if it is safe to call GetIntermediateData method. More... | |
| void | ResetIntermediateData (void) |
| Reset IntermediateData data member. More... | |
| const TIntermediateData & | GetIntermediateData (void) const |
| Get the IntermediateData member data. More... | |
| void | SetIntermediateData (TIntermediateData &value) |
| Assign a value to IntermediateData data member. More... | |
| TIntermediateData & | SetIntermediateData (void) |
| Assign a value to IntermediateData data member. More... | |
| bool | IsSetFinalData (void) const |
| Final representation for the PSSM Check if a value has been assigned to FinalData data member. More... | |
| bool | CanGetFinalData (void) const |
| Check if it is safe to call GetFinalData method. More... | |
| void | ResetFinalData (void) |
| Reset FinalData data member. More... | |
| const TFinalData & | GetFinalData (void) const |
| Get the FinalData member data. More... | |
| void | SetFinalData (TFinalData &value) |
| Assign a value to FinalData data member. More... | |
| TFinalData & | SetFinalData (void) |
| Assign a value to FinalData 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 | |
| CPssm_Base (const CPssm_Base &) | |
| CPssm_Base & | operator= (const CPssm_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| bool | m_IsProtein |
| CRef< TIdentifier > | m_Identifier |
| int | m_NumRows |
| int | m_NumColumns |
| list< string > | m_RowLabels |
| bool | m_ByRow |
| CRef< TQuery > | m_Query |
| CRef< TIntermediateData > | m_IntermediateData |
| CRef< TFinalData > | m_FinalData |
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
Position-specific scoring matrix.
Column indices on the PSSM refer to the positions corresponding to the query/master sequence, i.e. the number of columns (N) is the same as the length of the query/master sequence. Row indices refer to individual amino acid types, i.e. the number of rows (M) is the same as the number of different residues in the alphabet we use. Consequently, row labels are amino acid identifiers.
PSSMs are stored as linear arrays of integers. By default, we store them column-by-column, M values for the first column followed by M values for the second column, and so on. In order to provide flexibility for external applications, the boolean field "byrow" is provided to specify the storage order.
The documentation for this class was generated from the following files:
