include/algo/structure/bma_refine/RefinerDefs.hpp File Reference

#include <vector>
#include <map>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <objects/cdd/Cdd.hpp>
#include <algo/structure/struct_util/su_block_multiple_alignment.hpp>
#include <algo/structure/struct_util/su_sequence_set.hpp>
#include <algo/structure/struct_util/struct_util.hpp>
#include <algo/structure/bma_refine/ColumnScorer.hpp>
#include <algo/structure/bma_refine/BlockBoundaryAlgorithm.hpp>
#include <algo/structure/bma_refine/diagnosticDefs.hpp>

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Classes
struct	LeaveOneOutParams
struct	BlockEditingParams
struct	TrialStats
struct	RefinerAU
Typedefs
typedef double	TScoreType
typedef void(*	TFProgressCallback )(int num)
typedef vector< Block::Range >	Ranges
typedef map< unsigned int, Ranges >	RangeMap
typedef multimap< TScoreType, RefinerAU >	RefinedAlignments
typedef RefinedAlignments::iterator	RefinedAlignmentsIt
typedef RefinedAlignments::const_iterator	RefinedAlignmentsCIt
typedef RefinedAlignments::reverse_iterator	RefinedAlignmentsRevIt
typedef RefinedAlignments::const_reverse_iterator	RefinedAlignmentsRevCIt
typedef RefinedAlignments::value_type	RefinedAlignmentsVT
Enumerations
enum	RefinerResultCode {   eRefinerResultOK = 0, eRefinerResultNoResults = 9, eRefinerResultCantReadCD = 10, eRefinerResultAlignmentUtilityError = 11,   eRefinerResultBadInputAlignmentUtilityError = 12, eRefinerResultRangeForRefinementError = 13, eRefinerResultRowSelectorError = 14, eRefinerResultInconsistentShrinkageSettings = 15,   eRefinerResultInvalidThresholdValue = 16, eRefinerResultInvalidExtraArg = 17, eRefinerResultInconsistentArgumentCombination = 18, eRefinerResultCantDoBlockEditing = 19,   eRefinerResultTrialInitializationError = 20, eRefinerResultTrialExecutionError = 21, eRefinerResultLeaveOneOutExecutionError = 22, eRefinerResultLeaveNOutExecutionError = 23,   eRefinerResultNoRowsToRefine = 24, eRefinerResultPhaseSkipped = 100 }
enum	RefinerRowSelectorCode { eRandomSelectionOrder = 0, eWorstScoreFirst, eBestScoreFirst }
Functions
	USING_SCOPE (struct_util)
Variables
	USING_NCBI_SCOPE
const TScoreType	REFINER_INVALID_SCORE = kMin_Int
int	refinerCallbackCounter

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Typedef Documentation

typedef map< unsigned int, Ranges > RangeMap

Definition at line 271 of file RefinerDefs.hpp.

typedef vector< Block::Range > Ranges

Definition at line 270 of file RefinerDefs.hpp.

typedef multimap< TScoreType, RefinerAU > RefinedAlignments

Definition at line 274 of file RefinerDefs.hpp.

typedef RefinedAlignments::const_iterator RefinedAlignmentsCIt

Definition at line 276 of file RefinerDefs.hpp.

typedef RefinedAlignments::iterator RefinedAlignmentsIt

Definition at line 275 of file RefinerDefs.hpp.

typedef RefinedAlignments::const_reverse_iterator RefinedAlignmentsRevCIt

Definition at line 278 of file RefinerDefs.hpp.

typedef RefinedAlignments::reverse_iterator RefinedAlignmentsRevIt

Definition at line 277 of file RefinerDefs.hpp.

typedef RefinedAlignments::value_type RefinedAlignmentsVT

Definition at line 279 of file RefinerDefs.hpp.

typedef void(* TFProgressCallback)(int num)

Definition at line 267 of file RefinerDefs.hpp.

typedef double TScoreType

Definition at line 57 of file RefinerDefs.hpp.

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Enumeration Type Documentation

enum RefinerResultCode

Enumerator: eRefinerResultOK  eRefinerResultNoResults  eRefinerResultCantReadCD  eRefinerResultAlignmentUtilityError  eRefinerResultBadInputAlignmentUtilityError  eRefinerResultRangeForRefinementError  eRefinerResultRowSelectorError  eRefinerResultInconsistentShrinkageSettings  eRefinerResultInvalidThresholdValue  eRefinerResultInvalidExtraArg  eRefinerResultInconsistentArgumentCombination  eRefinerResultCantDoBlockEditing  eRefinerResultTrialInitializationError  eRefinerResultTrialExecutionError  eRefinerResultLeaveOneOutExecutionError  eRefinerResultLeaveNOutExecutionError  eRefinerResultNoRowsToRefine  eRefinerResultPhaseSkipped  Definition at line 61 of file RefinerDefs.hpp.

enum RefinerRowSelectorCode

Enumerator: eRandomSelectionOrder  eWorstScoreFirst  eBestScoreFirst  Definition at line 82 of file RefinerDefs.hpp.

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Function Documentation

USING_SCOPE (  struct_util   )

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Variable Documentation

const TScoreType REFINER_INVALID_SCORE = kMin_Int

Definition at line 58 of file RefinerDefs.hpp. Referenced by CBMARefinerTrial::DoTrial(), CBMARefinerEngine::GetBestRefinedAlignment(), CBMARefinerTrial::GetFinalScore(), CBMARefinerEngine::GetFinalScore(), CBMARefinerCycle::GetFinalScore(), CBMARefinerTrial::GetInitialScore(), CBMARefinerEngine::GetInitialScore(), CBMARefinerCycle::GetInitialScore(), CBMARefinerEngine::Refine(), and CBMARefinerPhase::ResetBase().

int refinerCallbackCounter

Definition at line 51 of file RefinerPhase.cpp. Referenced by CBMARefinerLOOPhase::DoPhase(), and CBMARefinerEngine::RunTrials().

USING_NCBI_SCOPE

Definition at line 52 of file RefinerDefs.hpp.

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