Class to handle the interaction with Alignment and statistics objects.
It serves as a wrapper or intermediate between the alignment and each specific stat.
It also encapsulates the similarityMatrix. More...

#include <Manager.h>

Public Member Functions
bool	setSimilarityMatrix (similarityMatrix *sm)
	Method to set a similarity matrix. More...

bool	calculateGapStats ()
	Method to handle gap stat calculation It checks if the gaps submodule has been created, otherwise, creates it. More...

void	printStatisticsGapsColumns ()
	Wrapper to Statistics::Gaps::printGapsColumns() It calls to calculateGapStats() to make sure the information is available before reporting the requested values. More...

void	printStatisticsGapsTotal ()
	Wrapper to Statistics::Gaps::printGapsAcl() It calls to calculateGapStats() to make sure the information is available before reporting the requested values. More...

bool	calculateConservationStats ()
	Method to handle similarity stat calculation It checks if the similarity submodule has been created, otherwise, creates it. More...

void	printStatisticsConservationColumns ()
	Wrapper to Statistics::Similarity::printConservationAcl() It calls to calculateConservationStats() to make sure the information is available before reporting the requested values. More...

void	printStatisticsConservationTotal ()
	Wrapper to Statistics::Similarity::printGapsTotal() It calls to calculateConservationStats() to make sure the information is available before reporting the requested values. More...

void	printCorrespondence ()
	Method to print the vector containing the keep/reject (Alignment::saveResidues) values of the associated Alignment If -1 , the residue would be rejected, otherwise, it prints the position on the alignment of the kept residue. More...

Public Attributes
Gaps *	gaps = nullptr
	Gaps submodule. More...

Similarity *	similarity = nullptr
	Similarity submodule. More...

Consistency *	consistency = nullptr
	Consistency submodule. More...

similarityMatrix *	_similarityMatrix = nullptr
	SimilarityMatrix used by Similarity. More...

int	ghWindow
	Gap window. More...

int	shWindow
	Similarity window. More...

Private Member Functions
	Manager (Alignment *parent)

	Manager (Alignment parent, Manager mold)

	~Manager ()

Private Attributes
Alignment *	alig

Friends
class	::Alignment

Detailed Description

Class to handle the interaction with Alignment and statistics objects.
It serves as a wrapper or intermediate between the alignment and each specific stat.
It also encapsulates the similarityMatrix.

Definition at line 53 of file Manager.h.

Constructor & Destructor Documentation

◆ Manager() [1/2]

statistics::Manager::Manager ( Alignment * parent )

explicitprivate

Definition at line 184 of file Manager.cpp.

References alig, ghWindow, and shWindow.

Referenced by Alignment::Alignment().

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◆ Manager() [2/2]

statistics::Manager::Manager	(	Alignment *	parent,
		Manager *	mold
	)

private

Definition at line 194 of file Manager.cpp.

Referenced by Alignment::Alignment().

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◆ ~Manager()

statistics::Manager::~Manager ( )

private

Definition at line 215 of file Manager.cpp.

References consistency, gaps, and similarity.

Member Function Documentation

◆ calculateConservationStats()

bool statistics::Manager::calculateConservationStats ( )

Method to handle similarity stat calculation
It checks if the similarity submodule has been created, otherwise, creates it.

Definition at line 36 of file Manager.cpp.

Referenced by Cleaner::clean(), Cleaner::cleanCombMethods(), Cleaner::cleanConservation(), printStatisticsConservationColumns(), and printStatisticsConservationTotal().

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◆ calculateGapStats()

bool statistics::Manager::calculateGapStats ( )

Method to handle gap stat calculation
It checks if the gaps submodule has been created, otherwise, creates it.

Definition at line 166 of file Manager.cpp.

References alig, statistics::Gaps::applyWindow(), statistics::Gaps::CalculateVectors(), gaps, statistics::Gaps::Gaps(), ghWindow, and Alignment::sequences.

Referenced by calculateConservationStats(), statistics::Similarity::calculateVectors(), Cleaner::clean(), Cleaner::clean2ndSlope(), Cleaner::cleanGaps(), Cleaner::cleanNoAllGaps(), printStatisticsGapsColumns(), printStatisticsGapsTotal(), and Cleaner::removeOnlyTerminal().

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◆ printCorrespondence()

void statistics::Manager::printCorrespondence ( )

Method to print the vector containing the keep/reject (Alignment::saveResidues) values of the associated Alignment
If -1 , the residue would be rejected, otherwise, it prints the position on the alignment of the kept residue.

Definition at line 144 of file Manager.cpp.

References alig, Alignment::originalNumberOfResidues, and Alignment::saveResidues.

Referenced by trimAlManager::innerPerform().

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◆ printStatisticsConservationColumns()

void statistics::Manager::printStatisticsConservationColumns ( )

Wrapper to Statistics::Similarity::printConservationAcl()
It calls to calculateConservationStats() to make sure the information is available before reporting the requested values.

Definition at line 73 of file Manager.cpp.

References alig, calculateConservationStats(), statistics::Similarity::printConservationColumns(), similarity, and Alignment::Statistics.

Referenced by trimAlManager::print_statistics().

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◆ printStatisticsConservationTotal()

void statistics::Manager::printStatisticsConservationTotal ( )

Wrapper to Statistics::Similarity::printGapsTotal()
It calls to calculateConservationStats() to make sure the information is available before reporting the requested values.

Definition at line 86 of file Manager.cpp.

References alig, calculateConservationStats(), statistics::Similarity::printConservationAcl(), similarity, and Alignment::Statistics.

Referenced by trimAlManager::print_statistics().

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◆ printStatisticsGapsColumns()

void statistics::Manager::printStatisticsGapsColumns ( )

Wrapper to Statistics::Gaps::printGapsColumns()
It calls to calculateGapStats() to make sure the information is available before reporting the requested values.

Definition at line 118 of file Manager.cpp.

References alig, calculateGapStats(), gaps, statistics::Gaps::printGapsColumns(), and Alignment::Statistics.

Referenced by trimAlManager::print_statistics().

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◆ printStatisticsGapsTotal()

void statistics::Manager::printStatisticsGapsTotal ( )

Wrapper to Statistics::Gaps::printGapsAcl()
It calls to calculateGapStats() to make sure the information is available before reporting the requested values.

Definition at line 131 of file Manager.cpp.

References alig, calculateGapStats(), gaps, statistics::Gaps::printGapsAcl(), and Alignment::Statistics.

Referenced by trimAlManager::print_statistics().

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◆ setSimilarityMatrix()

bool statistics::Manager::setSimilarityMatrix ( similarityMatrix * sm )

Method to set a similarity matrix.

Definition at line 100 of file Manager.cpp.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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Friends And Related Function Documentation

◆ ::Alignment

friend class ::Alignment

friend

Making Alignment a friend class allows us to have private constructor and destructors.
This gives us more control over the statistics classes, hinting that they shouldn't be created outside the scope of a newAlignmet.

Definition at line 133 of file Manager.h.

Member Data Documentation

◆ _similarityMatrix

similarityMatrix* statistics::Manager::_similarityMatrix = nullptr

SimilarityMatrix used by Similarity.

Definition at line 72 of file Manager.h.

Referenced by calculateConservationStats(), Manager(), and setSimilarityMatrix().

◆ alig

Alignment* statistics::Manager::alig

private

Definition at line 135 of file Manager.h.

Referenced by calculateConservationStats(), calculateGapStats(), Manager(), printCorrespondence(), printStatisticsConservationColumns(), printStatisticsConservationTotal(), printStatisticsGapsColumns(), printStatisticsGapsTotal(), and setSimilarityMatrix().

◆ consistency

Consistency* statistics::Manager::consistency = nullptr

Consistency submodule.

Definition at line 67 of file Manager.h.

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), trimAlManager::CleanResiduesNonAuto(), Manager(), statistics::Consistency::perform(), trimAlManager::print_statistics(), Alignment::statSVG(), and ~Manager().

◆ gaps

Gaps* statistics::Manager::gaps = nullptr

Gaps submodule.

Definition at line 59 of file Manager.h.

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), calculateGapStats(), statistics::Similarity::calculateVectors(), Cleaner::clean(), Cleaner::clean2ndSlope(), Cleaner::cleanCombMethods(), Cleaner::cleanGaps(), Cleaner::cleanNoAllGaps(), trimAlManager::CleanSequences(), Manager(), printStatisticsGapsColumns(), printStatisticsGapsTotal(), Cleaner::removeOnlyTerminal(), Alignment::statSVG(), and ~Manager().

◆ ghWindow

int statistics::Manager::ghWindow

Gap window.

Definition at line 77 of file Manager.h.

Referenced by calculateGapStats(), Manager(), and Alignment::setWindowsSize().

◆ shWindow

int statistics::Manager::shWindow

Similarity window.

Definition at line 81 of file Manager.h.

Referenced by calculateConservationStats(), Manager(), and Alignment::setWindowsSize().

◆ similarity

Similarity* statistics::Manager::similarity = nullptr

Similarity submodule.

Definition at line 63 of file Manager.h.

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), calculateConservationStats(), Cleaner::clean(), Cleaner::cleanCombMethods(), Cleaner::cleanConservation(), trimAlManager::CleanSequences(), Manager(), printStatisticsConservationColumns(), printStatisticsConservationTotal(), setSimilarityMatrix(), Alignment::statSVG(), and ~Manager().

The documentation for this class was generated from the following files:

/home/vfernandez/git/MyFork/include/Statistics/Manager.h
/home/vfernandez/git/MyFork/source/Statistics/Manager.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Manager() [1/2]

◆ Manager() [2/2]

◆ ~Manager()

Member Function Documentation

◆ calculateConservationStats()

◆ calculateGapStats()

◆ printCorrespondence()

◆ printStatisticsConservationColumns()

◆ printStatisticsConservationTotal()

◆ printStatisticsGapsColumns()

◆ printStatisticsGapsTotal()

◆ setSimilarityMatrix()

Friends And Related Function Documentation

◆ ::Alignment

Member Data Documentation

◆ _similarityMatrix

◆ alig

◆ consistency

◆ gaps

◆ ghWindow

◆ shWindow

◆ similarity