Submodule contained by Alignment . More...

#include <Cleaner.h>

Public Member Functions
int	selectMethod ()
	Method that selects the best cleaning method based on statistics of the alignment. More...

Alignment *	cleanByCutValueOverpass (double cut, float baseLine, const int *gInCol, bool complementary)
	Method to clean an alignment. It removes sequences that overpass or equals a certain threshold. The function detects if it would clean too many sequences, and relaxes the threshold until we have enough sequences to achieve the given percentage desired to keep. To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one. . More...

Alignment *	cleanByCutValueFallBehind (float cut, float baseLine, const float *ValueVect, bool complementary)
	Method to clean an alignment. It removes sequences that fall behind a certain threshold. The function detects if it would clean too many sequences, and relaxes the threshold until we have enough sequences to achieve the given percentage desired to keep. To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one. More...

Alignment *	cleanByCutValueOverpassOrEquals (double cutGaps, const int gInCol, float baseLine, float cutCons, const float MDK_Win, bool complementary)
	Method to clean an alignment. It removes sequences that overpass or equals the gap threshold but fall behind the similarity threshold. The function detects if it would clean too many sequences, and relaxes both thresholds until we have enough sequences to achieve the given percentage desired to keep. To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one. More...

Alignment *	cleanStrict (int gapCut, const int gInCol, float simCut, const float MDK_W, bool complementary, bool variable)
	Method to clean an alignment. It carries out strict and strictplus. It removes sequences that overpass the gap threshold but fall behind the similarity threshold. The function recovers those columns that, by themselves would be rejected, but it's neighbours (3 of 4) don't. Column blocks that don't have a minimum size set by the method itself, will be removed too. More...

Alignment *	cleanOverlapSeq (float minimumOverlap, float *overlapSeq, bool complementary)
	Method to trim an alignment based on a minimum sequence overlap threshold. The method selects a combination of parameters to maximize the final number of columns in the new alignment. . More...

Alignment *	cleanGaps (float baseLine, float gapsPct, bool complementary)
	Method to trim an alignment based on the gap distribution values. Column blocks that don't have a minimum size set by the method itself, will be removed too. More...

Alignment *	cleanConservation (float baseLine, float conservationPct, bool complementary)
	Method to trim an alignment based on the similarity distribution values. More...

Alignment *	clean (float baseLine, float GapsPct, float conservationPct, bool complementary)
	Method to trim an alignment based on the similarity and gaps distribution values. . More...

Alignment *	cleanCompareFile (float cutpoint, float baseLine, float *vectValues, bool complementary)
	Method to trim an alignment based on consistency values obtained from a dataset of alignments. The function computes the optimal parameter combination values to trim an alignment based on the consistency value from the comparison among a dataset of alignments with the same sequences. More...

bool	calculateSpuriousVector (float overlap, float *spuriousVector)
	Method to compute the overlap values. See Alignment::overlaps. More...

Alignment *	cleanSpuriousSeq (float overlapColumn, float minimumOverlap, bool complementary)
	Method to remove sequences missaligned with the rest of sequences in the alignment. For each residue in the sequence, it tests it's similarity. If the similarity of that residue is higher than overlapColumn value, it counts as a hit for the sequence. After calculating the number of hits for the sequence, it removes the sequence if it has a proportion hits/residues lower tan minimumOverlap. More...

Alignment *	clean2ndSlope (bool complementary)
	Method that carries the gappyout approach. This methods calculates the slope in gaps distribution on the original alignment. Then, it compares groups of three consecutive residues, searching for the group with the most abrupt change in slope. When found, the first residue is taken as the cutpoint for the sequences. More...

Alignment *	cleanCombMethods (bool complementary, bool variable)
	Method to clean an alignment. It carries out strict and strictplus. The method: More...

Alignment *	cleanNoAllGaps (bool complementary)
	Method to remove columns composed only by gaps This method is specially useful when we remove missaligned sequences from a given alignment. More...

Alignment *	removeColumns (int *columns, int init, int size, bool complementary)
	Method to remove columns, expressed as ranges. More...

Alignment *	removeSequences (int *seqs, int init, int size, bool complementary)
	Method to remove sequences, expressed as ranges. More...

Alignment *	getClustering (float identityThreshold)
	Method to select the most representative sequence (the longest one) for each cluster from the input alignment to generate a new alignment. More...

float	getCutPointClusters (int clusterNumber)
	Method that calculates the optimal cut point for a given clusters number. The idea is to obtain a cutpoint that can be used to obtain as sequences as clusterNumber. More...

void	removeSmallerBlocks (int blockSize, Alignment &original)
	Method to remove blocks of columns with no rejected residue smaller than a given size. More...

bool	removeOnlyTerminal ()
	Method to detect right and left borders. Borders are the first column found with no gaps. Everything between the borders are kept in the trimmed alignments. More...

void	removeAllGapsSeqsAndCols (bool seqs=true, bool cols=true)
	Method that identifies and removes columns and sequences composed only by gaps. More...

void	setTrimTerminalGapsFlag (bool terminalOnly_)
	Setter method to Terminal Only Flag. More...

void	setBoundaries (int *boundaries)
	Boundaries setter. More...

void	calculateSeqIdentity ()
	Method to calculate identities between the sequences from the alignment. See Alignment::identities. More...

void	calculateRelaxedSeqIdentity ()
	Method that makes a raw approximation of sequence identity computation. . More...

int *	calculateRepresentativeSeq (float maximumIdent)
	Method to assign sequences to clusters. Clusters are calculated following this flow: More...

void	computeComplementaryAlig (bool residues, bool sequences)
	Method for computing the complementary alignment. Complementary alignment is an alignment containing all sequences and columns that the original alignment would reject. It inverses the saveResidues / saveSequences tags. More...

void	removeDuplicates ()

Public Attributes
bool	terminalGapOnly
	Flag for trimming only on the terminal positions. More...

bool	keepSequences
	Flag for keeping sequences even when they are composed only by gaps. More...

int	blockSize
	Block size to use on the cleaning methods. More...

int	left_boundary
	left boundary of the alignment More...

int	right_boundary
	right boundary of the alignment More...

Private Member Functions
	Cleaner (Alignment *parent)
	Class Constructor - Called by Alignment. More...

	Cleaner (Alignment parent, Cleaner mold)
	Copy Constructor - Called by Alignment. More...

Private Attributes
Alignment *	alig
	Pointer to the alignment that contains this object. More...

Friends
class	Alignment

Detailed Description

Submodule contained by Alignment .

Complementary parameter: Cleaning methods may contain a boolean flag argument called 'complementary' .
If set to true, the function will return a new alignment that contains the sequences and residues that method would reject.
Otherwise it returns the cleaned version of the original alignment this object belongs to.

The use of this flag - complementary - is not recommended.
Complementarity is now performed when ALL methods have been applied.

Definition at line 52 of file Cleaner.h.

Constructor & Destructor Documentation

◆ Cleaner() [1/2]

Cleaner::Cleaner ( Alignment * parent )

explicitprivate

Class Constructor - Called by Alignment.

Definition at line 1633 of file Cleaner.cpp.

References alig, blockSize, keepSequences, left_boundary, right_boundary, and terminalGapOnly.

Referenced by Alignment::Alignment().

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◆ Cleaner() [2/2]

Cleaner::Cleaner	(	Alignment *	parent,
		Cleaner *	mold
	)

private

Copy Constructor - Called by Alignment.

Definition at line 1648 of file Cleaner.cpp.

References alig, blockSize, keepSequences, left_boundary, right_boundary, and terminalGapOnly.

Referenced by Alignment::Alignment().

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Member Function Documentation

◆ calculateRelaxedSeqIdentity()

void Cleaner::calculateRelaxedSeqIdentity ( )

Method that makes a raw approximation of sequence identity computation.
.

Warning: Not In Use

Note: Designed for reducing comparisons for huge alignments.

Definition at line 1483 of file Cleaner.cpp.

References alig, Alignment::identities, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, Alignment::saveResidues, Alignment::saveSequences, and Alignment::sequences.

◆ calculateRepresentativeSeq()

int * Cleaner::calculateRepresentativeSeq ( float maximumIdent )

Method to assign sequences to clusters.
Clusters are calculated following this flow:

Select the longest sequence and use it as representative of the first cluster.
Using the previously computed identity values, check if second longest sequence should be part of cluster of first sequence. This is computed using the identity value in comparison with a threshold.
If the second sequence should be part of the existing cluster, we add it. Otherwise we create a new cluster and use this sequence as representative for this new cluster.
Continue with the rest of sequences, comparing them with the representatives of existing clusters. If a sequence can pertain to more than one cluster, we choose the one that maximizes the identity value with the representative sequence.
Parameters

maximumIdent Identity threshold used to decide if a sequence should be part of a cluster or create a new one.

Returns
Vector that contains the clustering info.
The first item in the vector contains it's size.

Definition at line 1525 of file Cleaner.cpp.

References alig, calculateSeqIdentity(), Alignment::Cleaning, Alignment::identities, Alignment::originalNumberOfSequences, utils::quicksort(), utils::removeCharacter(), Alignment::saveSequences, and Alignment::sequences.

Referenced by getClustering().

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◆ calculateSeqIdentity()

void Cleaner::calculateSeqIdentity ( )

Method to calculate identities between the sequences from the alignment.
See Alignment::identities.

Definition at line 1434 of file Cleaner.cpp.

References AA, alig, Alignment::getAlignmentType(), Alignment::identities, Alignment::numberOfResidues, Alignment::originalNumberOfSequences, Alignment::saveResidues, Alignment::saveSequences, and Alignment::sequences.

Referenced by calculateRepresentativeSeq(), getCutPointClusters(), Alignment::printSeqIdentity(), and selectMethod().

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◆ calculateSpuriousVector()

bool Cleaner::calculateSpuriousVector	(	float	overlap,
		float *	spuriousVector
	)

Method to compute the overlap values.
See Alignment::overlaps.

Parameters

	overlap	Overlap threshold.
[out]	spuriousVector	Pointer to the spuriousVector to fill.

Returns: True if the calculation went ok.
False otherwise.
This should happen only if you pass a null pointer instead of a spuriousVector.

Definition at line 855 of file Cleaner.cpp.

References AA, alig, Alignment::getAlignmentType(), Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, and Alignment::sequences.

Referenced by cleanSpuriousSeq().

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◆ clean()

Alignment * Cleaner::clean	(	float	baseLine,
		float	GapsPct,
		float	conservationPct,
		bool	complementary
	)

Method to trim an alignment based on the similarity and gaps distribution values.
.

Parameters

baseLine	Minimum percentage of columns to conserve in the new alignment.
GapsPct	Maximum percentage of gaps per column.
conservationPct	Minimum value of similarity per column to keep the column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Take in mind: If baseLine is too strict, the other two will be relaxed to obtain the minimum percentage desired.

Returns: Pointer to the cleaned alignment.

Definition at line 784 of file Cleaner.cpp.

References alig, statistics::Gaps::calcCutPoint(), statistics::Similarity::calcCutPoint(), statistics::Manager::calculateConservationStats(), statistics::Manager::calculateGapStats(), cleanByCutValueOverpassOrEquals(), statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), statistics::Similarity::getMdkWindowedVector(), statistics::Manager::similarity, and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesNonAuto().

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◆ clean2ndSlope()

Alignment * Cleaner::clean2ndSlope ( bool complementary )

Method that carries the gappyout approach.
This methods calculates the slope in gaps distribution on the original alignment.
Then, it compares groups of three consecutive residues, searching for the group with the most abrupt change in slope.
When found, the first residue is taken as the cutpoint for the sequences.

Parameters

complementary Whether or not to return the complementary version of the trimmed alignment.

Definition at line 957 of file Cleaner.cpp.

References alig, statistics::Gaps::calcCutPoint2ndSlope(), statistics::Manager::calculateGapStats(), cleanByCutValueOverpass(), statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesAuto().

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◆ cleanByCutValueFallBehind()

Alignment * Cleaner::cleanByCutValueFallBehind	(	float	cut,
		float	baseLine,
		const float *	ValueVect,
		bool	complementary
	)

Method to clean an alignment.
It removes sequences that fall behind a certain threshold.
The function detects if it would clean too many sequences, and relaxes the threshold until we have enough sequences to achieve the given percentage desired to keep.
To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one.

Parameters

cut	Gap cut value to use.
baseLine	Percent of sequences to keep
ValueVect	Vector that contains the gaps present on each column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 231 of file Cleaner.cpp.

References alig, Alignment::Alignment(), blockSize, Alignment::Cleaning, Alignment::numberOfResidues, Alignment::originalNumberOfResidues, removeAllGapsSeqsAndCols(), removeSmallerBlocks(), utils::roundInt(), and Alignment::saveResidues.

Referenced by cleanCompareFile(), and cleanConservation().

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◆ cleanByCutValueOverpass()

Alignment * Cleaner::cleanByCutValueOverpass	(	double	cut,
		float	baseLine,
		const int *	gInCol,
		bool	complementary
	)

Method to clean an alignment.
It removes sequences that overpass or equals a certain threshold.
The function detects if it would clean too many sequences, and relaxes the threshold until we have enough sequences to achieve the given percentage desired to keep.
To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one.
.

Parameters

cut	Cut value to use. If a column has a value lower or equal to the cut value, it is removed.
baseLine	Percent of sequences to keep
gInCol	Vector that contains the values that will be tested for each column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 90 of file Cleaner.cpp.

References alig, Alignment::Alignment(), blockSize, Alignment::Cleaning, Alignment::numberOfResidues, Alignment::originalNumberOfResidues, utils::quicksort(), removeAllGapsSeqsAndCols(), removeSmallerBlocks(), utils::roundInt(), and Alignment::saveResidues.

Referenced by clean2ndSlope(), cleanGaps(), and cleanNoAllGaps().

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◆ cleanByCutValueOverpassOrEquals()

Alignment * Cleaner::cleanByCutValueOverpassOrEquals	(	double	cutGaps,
		const int *	gInCol,
		float	baseLine,
		float	cutCons,
		const float *	MDK_Win,
		bool	complementary
	)

Method to clean an alignment.
It removes sequences that overpass or equals the gap threshold but fall behind the similarity threshold.
The function detects if it would clean too many sequences, and relaxes both thresholds until we have enough sequences to achieve the given percentage desired to keep.
To achieve this, the method starts in the middle of the sequence and, alternating sides, adds column one by one.

Parameters

cutGaps	Gap cut value to use.
baseLine	Percent of sequences to keep
gInCol	Vector that contains the gaps present on each column.
MDK_Win	Vector that contains similarity value for each column.
cutCons	Minimum similarity value to keep a column in the alignment.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 357 of file Cleaner.cpp.

References alig, Alignment::Alignment(), blockSize, Alignment::Cleaning, Alignment::numberOfResidues, Alignment::originalNumberOfResidues, utils::quicksort(), removeAllGapsSeqsAndCols(), removeSmallerBlocks(), utils::roundInt(), and Alignment::saveResidues.

Referenced by clean().

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◆ cleanCombMethods()

Alignment * Cleaner::cleanCombMethods	(	bool	complementary,
		bool	variable
	)

Method to clean an alignment. It carries out strict and strictplus.
The method:

Computes gaps values and gap cut point of the alignment.
Computes similarity values and similarity cut point of the alignment.

Calls the cleanStrict method with these values and returns its output.

Parameters

complementary	Whether or not to return the complementary version of the trimmed alignment.
variable	Whether to use a variable block length. If false, block will be size 5. Else, it will use 1% of the alignment length, with a minimum of 3 and maximum of 12. This value will be overwritten if blockSize (of this object) is bigger than 0.

Returns: Pointer to the cleaned alignment returned by cleanStrict using the parameters calculated in this function.

Definition at line 980 of file Cleaner.cpp.

References alig, statistics::Gaps::calcCutPoint2ndSlope(), statistics::Manager::calculateConservationStats(), cleanStrict(), statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), statistics::Similarity::getMdkWindowedVector(), utils::initlVect(), Alignment::originalNumberOfResidues, utils::quicksort(), Alignment::saveResidues, statistics::Manager::similarity, and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesAuto().

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◆ cleanCompareFile()

Alignment * Cleaner::cleanCompareFile	(	float	cutpoint,
		float	baseLine,
		float *	vectValues,
		bool	complementary
	)

Method to trim an alignment based on consistency values obtained from a dataset of alignments.
The function computes the optimal parameter combination values to trim an alignment based on the consistency value from the comparison among a dataset of alignments with the same sequences.

Parameters

cutpoint	Hint of Gap cut point. May be used if it's lower than the minimum percentage threshold.
baseLine	Minimum percentage of columns to conserve in the new alignment.
vectValues	Vector with alignment consistency values
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 820 of file Cleaner.cpp.

References alig, cleanByCutValueFallBehind(), utils::copyVect(), utils::min(), Alignment::originalNumberOfResidues, and utils::quicksort().

Referenced by trimAlManager::CleanResiduesNonAuto().

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◆ cleanConservation()

Alignment * Cleaner::cleanConservation	(	float	baseLine,
		float	conservationPct,
		bool	complementary
	)

Method to trim an alignment based on the similarity distribution values.

Parameters

baseLine	Minimum percentage of columns to conserve in the new alignment.
conservationPct	Minimum value of similarity per column to keep the column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 760 of file Cleaner.cpp.

References alig, statistics::Similarity::calcCutPoint(), statistics::Manager::calculateConservationStats(), cleanByCutValueFallBehind(), statistics::Similarity::getMdkWindowedVector(), statistics::Manager::similarity, and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesNonAuto().

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◆ cleanGaps()

Alignment * Cleaner::cleanGaps	(	float	baseLine,
		float	gapsPct,
		bool	complementary
	)

Method to trim an alignment based on the gap distribution values. Column blocks that don't have a minimum size set by the method itself, will be removed too.

Parameters

baseLine	Minimum percentage of columns to conserve in the new alignment.
gapsPct	Maximum percentage of gaps per column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 736 of file Cleaner.cpp.

References alig, statistics::Gaps::calcCutPoint(), statistics::Manager::calculateGapStats(), cleanByCutValueOverpass(), statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesAuto(), and trimAlManager::CleanResiduesNonAuto().

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◆ cleanNoAllGaps()

Alignment * Cleaner::cleanNoAllGaps ( bool complementary )

Method to remove columns composed only by gaps
This method is specially useful when we remove missaligned sequences from a given alignment.

Parameters

complementary Whether or not to return the complementary version of the trimmed alignment.
Although this method contains a complementary flag, setting this up would return an alignment full of gaps-only columns.

Definition at line 1049 of file Cleaner.cpp.

References alig, statistics::Manager::calculateGapStats(), cleanByCutValueOverpass(), statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), Alignment::originalNumberOfSequences, and Alignment::Statistics.

Referenced by trimAlManager::CleanResiduesAuto(), and trimAlManager::CleanSequences().

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◆ cleanOverlapSeq()

Alignment * Cleaner::cleanOverlapSeq	(	float	minimumOverlap,
		float *	overlapSeq,
		bool	complementary
	)

Method to trim an alignment based on a minimum sequence overlap threshold.
The method selects a combination of parameters to maximize the final number of columns in the new alignment.
.

Parameters

minimumOverlap	Min overlap to keep a sequence.
overlapSeq	Vector containing the overlap for each column.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment.

Definition at line 714 of file Cleaner.cpp.

References alig, Alignment::Alignment(), Alignment::Cleaning, Alignment::originalNumberOfSequences, removeAllGapsSeqsAndCols(), and Alignment::saveSequences.

Referenced by cleanSpuriousSeq().

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◆ cleanSpuriousSeq()

Alignment * Cleaner::cleanSpuriousSeq	(	float	overlapColumn,
		float	minimumOverlap,
		bool	complementary
	)

Method to remove sequences missaligned with the rest of sequences in the alignment.
For each residue in the sequence, it tests it's similarity. If the similarity of that residue is higher than overlapColumn value, it counts as a hit for the sequence.
After calculating the number of hits for the sequence, it removes the sequence if it has a proportion hits/residues lower tan minimumOverlap.

Parameters

overlapColumn	Minimum similarity value that a residue needs to be considered a hit.
minimumOverlap	Minimum proportion of hits that a sequence needs to be kept in the new alignment.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Returns: Pointer to the cleaned alignment. \

Definition at line 934 of file Cleaner.cpp.

References alig, calculateSpuriousVector(), cleanOverlapSeq(), and Alignment::originalNumberOfSequences.

Referenced by trimAlManager::CleanSequences().

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◆ cleanStrict()

Alignment * Cleaner::cleanStrict	(	int	gapCut,
		const int *	gInCol,
		float	simCut,
		const float *	MDK_W,
		bool	complementary,
		bool	variable
	)

Method to clean an alignment. It carries out strict and strictplus.
It removes sequences that overpass the gap threshold but fall behind the similarity threshold.
The function recovers those columns that, by themselves would be rejected, but it's neighbours (3 of 4) don't.
Column blocks that don't have a minimum size set by the method itself, will be removed too.

Parameters

gapCut	Gap cut value to use.
gInCol	Vector that contains the gaps present on each column.
simCut	Minimum similarity value to keep a column.
MDK_W	Vector that contains the similarity of each column.
complementary	Whether or not to return the complementary version of the trimmed alignment.
variable	Whether to use a variable block length. If false, block will be size 5. Else, it will use 1% of the alignment length, with a minimum of 3 and maximum of 12. This value will be overwritten if blockSize (of this object) is bigger than 0.

Returns: Pointer to the cleaned alignment.

Definition at line 513 of file Cleaner.cpp.

References alig, Alignment::Alignment(), blockSize, Alignment::Cleaning, Alignment::numberOfResidues, Alignment::originalNumberOfResidues, removeAllGapsSeqsAndCols(), utils::roundInt(), and Alignment::saveResidues.

Referenced by cleanCombMethods().

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◆ computeComplementaryAlig()

void Cleaner::computeComplementaryAlig	(	bool	residues,
		bool	sequences
	)

Method for computing the complementary alignment.
Complementary alignment is an alignment containing all sequences and columns that the original alignment would reject.
It inverses the saveResidues / saveSequences tags.

Parameters

residues	Whether to reverse resiudes tags.
sequences	Whether to reverse sequences tags.

Definition at line 1589 of file Cleaner.cpp.

References alig, Alignment::numberOfResidues, Alignment::numberOfSequences, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, Alignment::saveResidues, and Alignment::saveSequences.

Referenced by trimAlManager::postprocess_alignment().

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◆ getClustering()

Alignment * Cleaner::getClustering ( float identityThreshold )

Method to select the most representative sequence (the longest one) for each cluster from the input alignment to generate a new alignment.

Parameters

identityThreshold Threshold used to assign sequences to clusters.
If identity between representative sequence of the cluster and sequence to assign is superior to this threshold and no other cluster has a better identity with its representative, it will be assigned to that cluster.

Definition at line 1211 of file Cleaner.cpp.

References alig, Alignment::Alignment(), calculateRepresentativeSeq(), Alignment::numberOfSequences, Alignment::originalNumberOfSequences, and Alignment::saveSequences.

Referenced by trimAlManager::CleanSequences().

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◆ getCutPointClusters()

float Cleaner::getCutPointClusters ( int clusterNumber )

Method that calculates the optimal cut point for a given clusters number.
The idea is to obtain a cutpoint that can be used to obtain as sequences as clusterNumber.

Parameters

clusterNumber Number of representative sequences to obtain.

Returns: CutPoint to obtain clusterNumber sequences.

Definition at line 1068 of file Cleaner.cpp.

References alig, calculateSeqIdentity(), Alignment::identities, Alignment::numberOfSequences, Alignment::originalNumberOfSequences, utils::quicksort(), utils::removeCharacter(), Alignment::saveSequences, and Alignment::sequences.

Referenced by trimAlManager::CleanSequences().

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◆ removeAllGapsSeqsAndCols()

void Cleaner::removeAllGapsSeqsAndCols	(	bool	seqs = `true`,
		bool	cols = `true`
	)

Method that identifies and removes columns and sequences composed only by gaps.

Definition at line 1367 of file Cleaner.cpp.

References alig, debug, KeepingOnlyGapsSequence, keepSequences, Alignment::numberOfResidues, Alignment::numberOfSequences, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, RemovingOnlyGapsSequence, reporting::reportManager::report(), Alignment::saveResidues, Alignment::saveSequences, Alignment::seqsName, and Alignment::sequences.

Referenced by cleanByCutValueFallBehind(), cleanByCutValueOverpass(), cleanByCutValueOverpassOrEquals(), cleanOverlapSeq(), cleanStrict(), removeColumns(), and removeSequences().

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◆ removeColumns()

Alignment * Cleaner::removeColumns	(	int *	columns,
		int	init,
		int	size,
		bool	complementary
	)

Method to remove columns, expressed as ranges.

Parameters

columns	Vector containing the columns to remove.
init	Where does the vector start. Set to 1 if the vector contains its size as first element.
size	Size of the columns vector.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Definition at line 1240 of file Cleaner.cpp.

References alig, Alignment::Alignment(), Alignment::Cleaning, removeAllGapsSeqsAndCols(), Alignment::saveResidues, and Alignment::updateSequencesAndResiduesNums().

Referenced by trimAlManager::CleanResiduesNonAuto().

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◆ removeDuplicates()

void Cleaner::removeDuplicates ( )

Definition at line 1610 of file Cleaner.cpp.

References alig, debug, Alignment::originalNumberOfSequences, RemovingDuplicateSequences, reporting::reportManager::report(), Alignment::saveSequences, Alignment::seqsName, and Alignment::sequences.

Referenced by trimAlManager::CleanSequences().

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◆ removeOnlyTerminal()

bool Cleaner::removeOnlyTerminal ( )

Method to detect right and left borders. Borders are the first column found with no gaps.
Everything between the borders are kept in the trimmed alignments.

Returns: True if everything went ok.
False if it was not possible to calculate the gap stats.

Definition at line 1283 of file Cleaner.cpp.

References alig, statistics::Manager::calculateGapStats(), debug, statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), left_boundary, LeftBoundaryBiggerThanRightBoundary, Alignment::originalNumberOfResidues, reporting::reportManager::report(), right_boundary, Alignment::saveResidues, Alignment::Statistics, and Alignment::updateSequencesAndResiduesNums().

Referenced by trimAlManager::postprocess_alignment().

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◆ removeSequences()

Alignment * Cleaner::removeSequences	(	int *	seqs,
		int	init,
		int	size,
		bool	complementary
	)

Method to remove sequences, expressed as ranges.

Parameters

seqs	Vector containing the sequences to remove.
init	Where does the vector start. Set to 1 if the vector contains its size as first element.
size	Size of the columns vector.
complementary	Whether or not to return the complementary version of the trimmed alignment.

Definition at line 1262 of file Cleaner.cpp.

References alig, Alignment::Alignment(), Alignment::Cleaning, removeAllGapsSeqsAndCols(), Alignment::saveSequences, and Alignment::updateSequencesAndResiduesNums().

Referenced by trimAlManager::CleanSequences().

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◆ removeSmallerBlocks()

void Cleaner::removeSmallerBlocks	(	int	blockSize,
		Alignment &	original
	)

Method to remove blocks of columns with no rejected residue smaller than a given size.

Parameters

blockSize	Minimum size to remove a block from the alignment
original	Alignment to apply the removal. Minimum size a block has to be to be kept.

Definition at line 1326 of file Cleaner.cpp.

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

Referenced by cleanByCutValueFallBehind(), cleanByCutValueOverpass(), and cleanByCutValueOverpassOrEquals().

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◆ selectMethod()

int Cleaner::selectMethod ( )

Method that selects the best cleaning method based on statistics of the alignment.

Definition at line 42 of file Cleaner.cpp.

References alig, calculateSeqIdentity(), Alignment::identities, and Alignment::numberOfSequences.

Referenced by trimAlManager::CleanResiduesAuto().

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◆ setBoundaries()

void Cleaner::setBoundaries ( int * boundaries )

Boundaries setter.

Warning: Not In Use

Parameters

[in] boundaries New boundaries values.

Definition at line 1201 of file Cleaner.cpp.

References left_boundary, and right_boundary.

◆ setTrimTerminalGapsFlag()

void Cleaner::setTrimTerminalGapsFlag ( bool terminalOnly_ )

Setter method to Terminal Only Flag.

Parameters

terminalOnly_ New vlue of the Terminal Only Flag.

Definition at line 1194 of file Cleaner.cpp.

References terminalGapOnly.

Referenced by trimAlManager::innerPerform().

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Friends And Related Function Documentation

◆ Alignment

friend class Alignment

friend

Definition at line 480 of file Cleaner.h.

Member Data Documentation

◆ alig

Alignment* Cleaner::alig

private

Pointer to the alignment that contains this object.

Definition at line 485 of file Cleaner.h.

Referenced by calculateRelaxedSeqIdentity(), calculateRepresentativeSeq(), calculateSeqIdentity(), calculateSpuriousVector(), clean(), clean2ndSlope(), cleanByCutValueFallBehind(), cleanByCutValueOverpass(), cleanByCutValueOverpassOrEquals(), cleanCombMethods(), cleanCompareFile(), cleanConservation(), Cleaner(), cleanGaps(), cleanNoAllGaps(), cleanOverlapSeq(), cleanSpuriousSeq(), cleanStrict(), computeComplementaryAlig(), getClustering(), getCutPointClusters(), removeAllGapsSeqsAndCols(), removeColumns(), removeDuplicates(), removeOnlyTerminal(), removeSequences(), removeSmallerBlocks(), and selectMethod().

◆ blockSize

int Cleaner::blockSize

Block size to use on the cleaning methods.

Definition at line 67 of file Cleaner.h.

Referenced by cleanByCutValueFallBehind(), cleanByCutValueOverpass(), cleanByCutValueOverpassOrEquals(), Cleaner(), cleanStrict(), and Alignment::setBlockSize().

◆ keepSequences

bool Cleaner::keepSequences

Flag for keeping sequences even when they are composed only by gaps.

Definition at line 63 of file Cleaner.h.

Referenced by Cleaner(), removeAllGapsSeqsAndCols(), and Alignment::setKeepSequencesFlag().

◆ left_boundary

int Cleaner::left_boundary

left boundary of the alignment

Definition at line 71 of file Cleaner.h.

Referenced by Cleaner(), removeOnlyTerminal(), and setBoundaries().

◆ right_boundary

int Cleaner::right_boundary

right boundary of the alignment

Definition at line 75 of file Cleaner.h.

Referenced by Cleaner(), removeOnlyTerminal(), and setBoundaries().

◆ terminalGapOnly

bool Cleaner::terminalGapOnly

Flag for trimming only on the terminal positions.

Definition at line 59 of file Cleaner.h.

Referenced by Cleaner(), and setTrimTerminalGapsFlag().

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

/home/vfernandez/git/MyFork/include/Cleaner.h
/home/vfernandez/git/MyFork/source/Cleaner.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Cleaner() [1/2]

◆ Cleaner() [2/2]

Member Function Documentation

◆ calculateRelaxedSeqIdentity()

◆ calculateRepresentativeSeq()

◆ calculateSeqIdentity()

◆ calculateSpuriousVector()

◆ clean()

◆ clean2ndSlope()

◆ cleanByCutValueFallBehind()

◆ cleanByCutValueOverpass()

◆ cleanByCutValueOverpassOrEquals()

◆ cleanCombMethods()

◆ cleanCompareFile()

◆ cleanConservation()

◆ cleanGaps()

◆ cleanNoAllGaps()

◆ cleanOverlapSeq()

◆ cleanSpuriousSeq()

◆ cleanStrict()

◆ computeComplementaryAlig()

◆ getClustering()

◆ getCutPointClusters()

◆ removeAllGapsSeqsAndCols()

◆ removeColumns()

◆ removeDuplicates()

◆ removeOnlyTerminal()

◆ removeSequences()

◆ removeSmallerBlocks()

◆ selectMethod()

◆ setBoundaries()

◆ setTrimTerminalGapsFlag()

Friends And Related Function Documentation

◆ Alignment

Member Data Documentation

◆ alig

◆ blockSize

◆ keepSequences

◆ left_boundary

◆ right_boundary

◆ terminalGapOnly