Class to calculate the consistency between several MSA containing the same sequences, differently aligned.
Using this statistics, the class is able to select the most consistent alignment between all alignments provided.
It is possible to forcefully select an alignment, but to calculate the statistics for latter use.
After selecting an alignment (most consistent or manually selected), it is possible to use this statistic to trim the alignment, removing columns that are not consistent enough with the other alignments. More...

#include <Consistency.h>

Public Member Functions
bool	perform (char comparesetFilePath, FormatHandling::FormatManager &formatManager, trimAlManager &manager, char forceFile)
	Method to compare a set of MSA, all containing the same sequences and residues. The number of residues must be the same, but gaps are not taken into account. This is due to the same sequence being aligned in different ways, which changes the gap patterns. More...

bool	applyWindow (int halfW)
	Applies a new window to the alignment. More...

	Consistency (Alignment pAlignment, Consistency pConsistency)
	Copy constructor. More...

	Consistency ()
	Default Construtor. More...

	~Consistency ()
	Default Destructor. More...

float *	getValues ()
	Stat Getter . More...

Static Public Member Functions
static void	printStatisticsFileColumns (Alignment &alig, float *compareVect)
	Print the consistency value for each column from the selected alignment. More...

static void	printStatisticsFileAcl (Alignment &alig, float *compareVect)
	Print the accumulated consistency value from the selected alignment. More...

Private Member Functions
bool	isWindowDefined ()
	Method to check wether or not a window has been applied. More...

Static Private Member Functions
static int	compareAndChoose (Alignment vectAlignments, char fileNames, float *columnsValue, int numAlignments, bool verbosity)
	Method to compare a set of alignments to select the most consistent one respect the others. To compute the consistency values we use the proportion of residue pairs per columns in the alignments to compare. More...

static bool	forceComparison (Alignment *vectAlignments, int numAlignments, Alignment selected, float *columnsValue)
	Method to obtain the consistency values vector for a given alignment against a set of alignments with the same sequences. More...

Private Attributes
Alignment *	alig = nullptr
	Original alignment for which the stat was calculated. More...

Alignment **	compareAlignmentsArray = nullptr
	Array of alignments to compare. More...

float *	values = nullptr
	Raw consistency values. More...

float *	values_windowed = nullptr
	Windowed consistency values. More...

int	numFiles = 0
	Number of files to compare. More...

int	i = 0
	Temporary variable used on loops. More...

int	maxResidues = 0
	Maximum number of residues on the whole dataset. More...

int	halfWindow = -1
	Variable to store the type of the alignment from the last alignment. More...

int	residues = -1
	Number of residues of the selected alignment. More...

int *	refCounter
	Counter of how many statisticsConsistency share the same MDK values. More...

bool	appearErrors = false
	Intermediate variable to keep track of the progress status. More...

Detailed Description

Class to calculate the consistency between several MSA containing the same sequences, differently aligned.
Using this statistics, the class is able to select the most consistent alignment between all alignments provided.
It is possible to forcefully select an alignment, but to calculate the statistics for latter use.
After selecting an alignment (most consistent or manually selected), it is possible to use this statistic to trim the alignment, removing columns that are not consistent enough with the other alignments.

Definition at line 58 of file Consistency.h.

Constructor & Destructor Documentation

◆ Consistency() [1/2]

statistics::Consistency::Consistency	(	Alignment *	pAlignment,
		Consistency *	pConsistency
	)

Copy constructor.

Definition at line 829 of file Consistency.cpp.

References alig, refCounter, values, and values_windowed.

Referenced by statistics::Manager::Manager().

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◆ Consistency() [2/2]

statistics::Consistency::Consistency ( )

Default Construtor.

Definition at line 839 of file Consistency.cpp.

References refCounter.

Referenced by trimAlManager::performCompareset().

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◆ ~Consistency()

statistics::Consistency::~Consistency ( )

Default Destructor.

Definition at line 820 of file Consistency.cpp.

References alig, refCounter, values, and values_windowed.

Member Function Documentation

◆ applyWindow()

bool statistics::Consistency::applyWindow ( int halfW )

Applies a new window to the alignment.

Parameters

halfW Half size of window to apply.

Returns: True if correct Exits if false

Definition at line 525 of file Consistency.cpp.

References ConsistencyWindowTooBig, debug, halfWindow, reporting::reportManager::report(), residues, values, and values_windowed.

Referenced by getValues(), and perform().

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◆ compareAndChoose()

int statistics::Consistency::compareAndChoose	(	Alignment **	vectAlignments,
		char **	fileNames,
		float *	columnsValue,
		int	numAlignments,
		bool	verbosity
	)

staticprivate

Method to compare a set of alignments to select the most consistent one respect the others.
To compute the consistency values we use the proportion of residue pairs per columns in the alignments to compare.

Parameters

	vectAlignments	Alignment vector to compare and select the most consistent.
	fileNames	Vector containing all the filenames. Useful only if verbosity==True.
[out]	columnsValue	Consistency values of selected alignment.
	numAlignments	Number of alignments to compare.
	verbosity	Wether or not report by printing some results.

Returns: -1 if there was any error.
Alignment index of the selected algorithm otherwise.

Definition at line 241 of file Consistency.cpp.

References debug, DifferentNumberOfSequencesInCompareset, DifferentSeqsNamesInCompareset, Alignment::sequencesMatrix::getColumn(), Alignment::getNumAminos(), Alignment::getNumSpecies(), Alignment::getSequenceNameOrder(), Alignment::getSequences(), utils::initlVect(), reporting::reportManager::report(), Alignment::SequencesMatrix, and Alignment::sequencesMatrix::setOrder().

Referenced by perform().

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◆ forceComparison()

bool statistics::Consistency::forceComparison	(	Alignment **	vectAlignments,
		int	numAlignments,
		Alignment *	selected,
		float *	columnsValue
	)

staticprivate

Method to obtain the consistency values vector for a given alignment against a set of alignments with the same sequences.

Parameters

	vectAlignments	Alignment vector to compare against the selected alignment
	numAlignments	Number of alignments to compare
	selected	Alignment to compare against the set of alignments.
[out]	columnsValue	Vector to fill with the consistency values.

Returns: Wether or not the method went ok.

Definition at line 416 of file Consistency.cpp.

References debug, DifferentNumberOfSequencesInCompareset, DifferentSeqsNamesInCompareset, Alignment::sequencesMatrix::getColumn(), Alignment::getNumAminos(), Alignment::getNumSpecies(), Alignment::getSequenceNameOrder(), Alignment::getSequences(), utils::initlVect(), reporting::reportManager::report(), Alignment::SequencesMatrix, Alignment::sequencesMatrix::sequencesMatrix(), and Alignment::sequencesMatrix::setOrder().

Referenced by perform().

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◆ getValues()

float * statistics::Consistency::getValues ( )

Stat Getter
.

Returns: If a window has been set and applied, it will return the windowed values If a window has been set, but not applied, it wil apply it and return the windowed values. If no window has been set, it will return the raw values.

Definition at line 588 of file Consistency.cpp.

References applyWindow(), halfWindow, isWindowDefined(), values, and values_windowed.

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), trimAlManager::CleanResiduesNonAuto(), trimAlManager::print_statistics(), and Alignment::statSVG().

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◆ isWindowDefined()

bool statistics::Consistency::isWindowDefined ( )

private

Method to check wether or not a window has been applied.

Returns: True halfWindow is different than -1

Definition at line 580 of file Consistency.cpp.

References halfWindow.

Referenced by getValues().

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◆ perform()

bool statistics::Consistency::perform	(	char *	comparesetFilePath,
		FormatHandling::FormatManager &	formatManager,
		trimAlManager &	manager,
		char *	forceFile
	)

Method to compare a set of MSA, all containing the same sequences and residues.
The number of residues must be the same, but gaps are not taken into account.
This is due to the same sequence being aligned in different ways, which changes the gap patterns.

Parameters

comparesetFilePath	Path to the file containing paths for each alignment to compare. One per line
formatManager	Format manager, to load and save the alignments.
manager	trimAl manager, to store the choosen alignment in trimAlManager::origAlig
forceFile	path to file to forcefully select. If nullptr, the most consistent alignment will be selected.

Note: The method does not return anything, as the alignment is stored on trimAlManager::origAlig It also stores the current instance of statisticsConsistency into the consistent alignment. This allows us to use this information to trim, or represent it on the HTML/SVG reports.

Definition at line 45 of file Consistency.cpp.

References alig, Alignment::Alignment(), AlignmentTypesNotMatching, trimAlManager::appearErrors, appearErrors, applyWindow(), compareAlignmentsArray, compareAndChoose(), ComparesetFailedAlignmentMissing, statistics::Manager::consistency, trimAlManager::consistencyWindow, trimAlManager::CS, debug, forceComparison(), Alignment::getAlignmentType(), FormatHandling::FormatManager::getFileFormatName(), Alignment::getNumAminos(), i, Alignment::isFileAligned(), FormatHandling::FormatManager::loadAlignment(), maxResidues, NotAligned, NotDefined, numFiles, trimAlManager::oformats, trimAlManager::origAlig, Alignment::originalNumberOfResidues, trimAlManager::outfile, reporting::reportManager::report(), residues, Alignment::SequencesMatrix, Alignment::sequencesMatrix::sequencesMatrix(), Alignment::Statistics, trimAlManager::stats, values, and trimAlManager::windowSize.

Referenced by trimAlManager::performCompareset().

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◆ printStatisticsFileAcl()

void statistics::Consistency::printStatisticsFileAcl	(	Alignment &	alig,
		float *	compareVect
	)

static

Print the accumulated consistency value from the selected alignment.

Parameters

alig	Alignment used to obtain the accumulated consistency value
compareVect	Vector containing the consistency value for each column.

Definition at line 666 of file Consistency.cpp.

References utils::copyVect(), Alignment::filename, Alignment::numberOfResidues, and utils::quicksort().

Referenced by trimAlManager::print_statistics().

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◆ printStatisticsFileColumns()

void statistics::Consistency::printStatisticsFileColumns	(	Alignment &	alig,
		float *	compareVect
	)

static

Print the consistency value for each column from the selected alignment.

Parameters

alig	Alignment used to obtain the accumulated consistency value
compareVect	Vector containing the consistency value for each column.

float* statistics::Consistency::values = nullptr

private

Raw consistency values.

Definition at line 133 of file Consistency.h.

Referenced by applyWindow(), Consistency(), getValues(), perform(), and ~Consistency().

◆ values_windowed

float* statistics::Consistency::values_windowed = nullptr

private

Windowed consistency values.

Definition at line 136 of file Consistency.h.

Referenced by applyWindow(), Consistency(), getValues(), and ~Consistency().

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Consistency() [1/2]

◆ Consistency() [2/2]

◆ ~Consistency()

Member Function Documentation

◆ applyWindow()

◆ compareAndChoose()

◆ forceComparison()

◆ getValues()

◆ isWindowDefined()

◆ perform()

◆ printStatisticsFileAcl()

◆ printStatisticsFileColumns()

Member Data Documentation

◆ alig

◆ appearErrors

◆ compareAlignmentsArray

◆ halfWindow

◆ i

◆ maxResidues

◆ numFiles

◆ refCounter

◆ residues

◆ values

◆ values_windowed