NCBI C++ ToolKit
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CdPssmInput Class Reference

Search Toolkit Book for CdPssmInput

#include <algo/structure/cd_utils/cuPssmMaker.hpp>

+ Inheritance diagram for CdPssmInput:
+ Collaboration diagram for CdPssmInput:

Public Member Functions

 CdPssmInput (ResidueProfiles &profiles, PssmMakerOptions &config, bool useConsensus)
 
 ~CdPssmInput ()
 
void read (ColumnResidueProfile &crp)
 
void Process ()
 Algorithm to produce multiple sequence alignment structure should be implemented in this method. More...
 
unsigned char * GetQuery ()
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
unsigned int GetQueryLength ()
 Get the query's length. More...
 
PSIMsaGetData ()
 Obtain the multiple sequence alignment structure. More...
 
const PSIBlastOptionsGetOptions ()
 Obtain the options for the PSSM engine. More...
 
PSIBlastOptionsSetOptions ()
 Obtain the options for the PSSM engine. More...
 
const char * GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
const PSIDiagnosticsRequestGetDiagnosticsRequest ()
 Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object. More...
 
- Public Member Functions inherited from IPssmInputData
virtual ~IPssmInputData ()
 virtual destructor More...
 
- Public Member Functions inherited from IPssmInput_Base
virtual ~IPssmInput_Base ()
 virtual destructor More...
 
virtual int GetGapExistence ()
 Obtain the gap existence value for the underlying matrix used to build the PSSM. More...
 
virtual int GetGapExtension ()
 Obtain the gap extension value for the underlying matrix used to build the PSSM. More...
 
virtual CRef< objects::CBioseq > GetQueryForPssm ()
 Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). More...
 
- 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
 
- Public Member Functions inherited from ColumnReader
virtual ~ColumnReader ()
 

Private Member Functions

void moveUpLongestRow ()
 
int countResiduesInRow (int row)
 
void copyRow (PSIMsaCell *src, PSIMsaCell *dest)
 
void unalignLeadingTrailingGaps ()
 

Private Attributes

ResidueProfilesm_profiles
 
PSIBlastOptionsm_options
 
bool m_useConsensus
 
PSIMsam_msa
 
PSIMsaDimensions m_msaDimensions
 Multiple sequence alignment dimensions. More...
 
PSIDiagnosticsRequest m_diagRequest
 
string m_matrixName
 
unsigned char * m_query
 
unsigned int m_queryLength
 
int m_currentCol
 

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 80 of file cuPssmMaker.hpp.

Constructor & Destructor Documentation

◆ CdPssmInput()

CdPssmInput::CdPssmInput ( ResidueProfiles profiles,
PssmMakerOptions config,
bool  useConsensus 
)

◆ ~CdPssmInput()

CdPssmInput::~CdPssmInput ( )

Definition at line 175 of file cuPssmMaker.cpp.

References m_msa, m_options, PSIBlastOptionsFree(), and PSIMsaFree().

Member Function Documentation

◆ copyRow()

void CdPssmInput::copyRow ( PSIMsaCell src,
PSIMsaCell dest 
)
private

◆ countResiduesInRow()

int CdPssmInput::countResiduesInRow ( int  row)
private

◆ GetData()

PSIMsa * CdPssmInput::GetData ( void  )
virtual

Obtain the multiple sequence alignment structure.

Implements IPssmInputData.

Definition at line 290 of file cuPssmMaker.cpp.

References m_msa.

Referenced by PssmMaker::getPssmColumnResidues(), PssmMaker::printAlignment(), and PssmMaker::printAlignmentByColumn().

◆ GetDiagnosticsRequest()

const PSIDiagnosticsRequest * CdPssmInput::GetDiagnosticsRequest ( void  )
virtual

Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object.

Reimplemented from IPssmInputData.

Definition at line 314 of file cuPssmMaker.cpp.

References m_diagRequest.

◆ GetMatrixName()

const char * CdPssmInput::GetMatrixName ( void  )
virtual

Obtain the name of the underlying matrix to use when building the PSSM.

Reimplemented from IPssmInput_Base.

Definition at line 307 of file cuPssmMaker.cpp.

References m_matrixName.

◆ GetOptions()

const PSIBlastOptions * CdPssmInput::GetOptions ( void  )
virtual

Obtain the options for the PSSM engine.

Implements IPssmInputData.

Definition at line 296 of file cuPssmMaker.cpp.

References m_options.

Referenced by PssmMaker::make().

◆ GetQuery()

unsigned char * CdPssmInput::GetQuery ( void  )
virtual

Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.

Implements IPssmInput_Base.

Definition at line 278 of file cuPssmMaker.cpp.

References m_query.

Referenced by PssmMaker::make().

◆ GetQueryLength()

unsigned int CdPssmInput::GetQueryLength ( void  )
virtual

Get the query's length.

Implements IPssmInput_Base.

Definition at line 284 of file cuPssmMaker.cpp.

References m_msaDimensions, and PSIMsaDimensions::query_length.

Referenced by PssmMaker::make().

◆ moveUpLongestRow()

void CdPssmInput::moveUpLongestRow ( )
private

◆ Process()

void CdPssmInput::Process ( )
virtual

Algorithm to produce multiple sequence alignment structure should be implemented in this method.

This will be invoked by the CPssmEngine object before calling GetData()

Implements IPssmInputData.

Definition at line 181 of file cuPssmMaker.cpp.

References PSIMsa::data, i, PSIMsaCell::is_aligned, PSIMsaCell::letter, m_msa, m_msaDimensions, m_profiles, m_query, m_useConsensus, PSIMsaDimensions::query_length, ResidueProfiles::traverseColumnsOnConsensus(), ResidueProfiles::traverseColumnsOnMaster(), and unalignLeadingTrailingGaps().

◆ read()

void CdPssmInput::read ( ColumnResidueProfile crp)
virtual

◆ SetOptions()

PSIBlastOptions * CdPssmInput::SetOptions ( void  )

Obtain the options for the PSSM engine.

Definition at line 302 of file cuPssmMaker.cpp.

References m_options.

◆ unalignLeadingTrailingGaps()

void CdPssmInput::unalignLeadingTrailingGaps ( )
private

Member Data Documentation

◆ m_currentCol

int CdPssmInput::m_currentCol
private

Definition at line 123 of file cuPssmMaker.hpp.

Referenced by read().

◆ m_diagRequest

PSIDiagnosticsRequest CdPssmInput::m_diagRequest
private

Definition at line 119 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), and GetDiagnosticsRequest().

◆ m_matrixName

string CdPssmInput::m_matrixName
private

Definition at line 120 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), and GetMatrixName().

◆ m_msa

PSIMsa* CdPssmInput::m_msa
private

◆ m_msaDimensions

PSIMsaDimensions CdPssmInput::m_msaDimensions
private

Multiple sequence alignment dimensions.

Definition at line 118 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), copyRow(), countResiduesInRow(), GetQueryLength(), moveUpLongestRow(), Process(), and unalignLeadingTrailingGaps().

◆ m_options

PSIBlastOptions* CdPssmInput::m_options
private

Definition at line 112 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), GetOptions(), SetOptions(), and ~CdPssmInput().

◆ m_profiles

ResidueProfiles& CdPssmInput::m_profiles
private

Definition at line 111 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), Process(), and read().

◆ m_query

unsigned char* CdPssmInput::m_query
private

Definition at line 121 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), GetQuery(), and Process().

◆ m_queryLength

unsigned int CdPssmInput::m_queryLength
private

Definition at line 122 of file cuPssmMaker.hpp.

◆ m_useConsensus

bool CdPssmInput::m_useConsensus
private

Definition at line 114 of file cuPssmMaker.hpp.

Referenced by CdPssmInput(), Process(), and read().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:01:29 2024 by modify_doxy.py rev. 669887