Class containing an alignment
This class stores the alignment sequences with it's names, residues and extra information.
It contains multiple methods regarding the sequences.
It also contains submodules that provide methods for Calculating statistics, Trim the alignment and Printing sequences information. More...

#include <Alignment.h>

Classes
class	sequencesMatrix
	Internal Alignment Class that represents a sequences matrix. More...

Public Member Functions
bool	fillMatrices (bool aligned, bool checkInvalidChars=true)
	Method to initialize matrices and check if the sequences have been correctly loaded and are free of errors It checks if sequences contain unknown characters, sets the isAligned flag and initializes 'saveResidues' and 'saveSequences', depending on the sizes of the sequences (whether or not they have the same length). More...

	Alignment ()
	Constructor. More...

	Alignment (Alignment &)
	Copy Constructor. The copy constructor does not make a copy of all structures present on the original alignment. Instead, all alignments that share a common origin, share some information, and also, a counter (Alignment::SeqRef) of how many alignments share the same information. This allows us to keep the information on memory while any alignment is using it. When an alignment is destroyed, the counter is substracted by 1, and, if it is 0 after the substraction, the shared data is destroyed. More...

	~Alignment ()
	Destructor. The destructor takes care of removing the non-shared information of each alignment when is destroyed. It also substracts 1 from the shared counter Alignment::SeqRef. When Alignment::SeqRef arrives to 0, the shared data is destroyed, including Alignment::SeqRef. More...

int	getNumSpecies ()
	Number of sequences getter. More...

void	getSequences (std::string *names)
	Getter for the sequences names. More...

void	getSequences (std::string names, int lenghts)
	Getter for the sequences names and its lenghts. More...

void	getSequences (std::string names, std::string sequences, int *lenghts)
	Getter for the sequences, its names and lenghts. More...

bool	getSequenceNameOrder (std::string names, int orderVector)
	Method to map two sets of sequences, own and external. The method accepts a vector of names, and test them against the alignment own sequences' names. If the sequence is present, its index will be stored in orderVector. . More...

int	getNumAminos ()
	Residues number getter. It counts gaps as residue. More...

void	setWindowsSize (int ghWindow, int shWindow)
	Windows setter. More...

void	setBlockSize (int blockSize)
	BlockSize Setter. More...

void	calculateSeqOverlap ()
	Calculates overlap between sequences. More...

void	printSeqIdentity ()
	Method to print different identity values computed from the alignment. In this method we assess the identity values matrix, as well as different average values. Moreover, the method computes which one is the most similar sequence. More...

void	printSeqOverlap ()
	Prints the overlap between sequences. More...

int	getAlignmentType () const
	Alignment type getter. See SequenceTypes. More...

bool	isFileAligned ()
	isAligned getter. More...

Alignment *	getTranslationCDS (Alignment *proteinAlignment)
	Method to back translate a protein alignment using the sequences present on the current alignment. Current alignment should contain the original sequences which were translated to protein sequences, without any gap. More...

bool	checkCorrespondence (std::string names, int lenghts, int totalInputSequences, int multiple)
	Function to check CDS file. . More...

void	calculateColIdentity (float *columnIdentity)
	Method that calculates the columns identity value. This is, the frequency of the most present element in the column, being residue, indetermination and gap allowed. More...

void	setKeepSequencesFlag (bool newFlagValue)
	Keep Sequences setter. More...

void	printAlignmentInfo (std::ostream &output)
	Print information about sequences number, average sequence length, maximum and minimum sequences length, etc. More...

bool	prepareCodingSequence (bool splitByStopCodon, bool ignoreStopCodon, Alignment *proteinAlignment)
	Method to check if the CDS file is correct. Based on nature of residues: DNA/RNA (Most of the residues) There is no gaps on the whole dataset. Each sequence is a multiple of 3. It will also remove or split stop codons depending on the flags passed. More...

bool	alignmentSummaryHTML (const Alignment &trimmedAlig, const char *const destFile)
	Method to report the trimming results in HTML. Outputs an HTML file that shows visually what has been done to the alignment (removed sequences or residues) and the stats used to do so. More...

bool	statSVG (const char *const destFile)

bool	alignmentSummarySVG (Alignment &trimmedAlig, const char *destFile, int blocks)
	Method to report the trimming results in SVG. Outputs a SVG file that shows visually what has been done to the alignment (removed sequences or residues) and the stats used to do so. More...

void	updateSequencesAndResiduesNums (bool countSequences=true, bool countResidues=true)
	Updates the sequence number and residue number based on saveResidues and saveSequences. More...

Public Attributes
Cleaner *	Cleaning = nullptr
	Trimming submodule. It contains methods and variables related to trimming. More...

statistics::Manager *	Statistics = nullptr
	Statistics submodule. It contains methods and variables related to statistics calculation and reporting. More...

sequencesMatrix *	SequencesMatrix = nullptr
	SequencesMatrix submodule This helper module stores the sequences without gaps. Useful when comparing MSA. More...

int *	SeqRef = nullptr
	Pointer to keep a count of how many alignments depend on the same shared-sequences. Increased on each trim step, and automatically reduced on each alignment destroy. If it arrives to 0, the last alignment being destroyed will also take care of releasing memory for shared information. More...

int	originalNumberOfSequences = 0
	Number of sequences the alignment had when it was loaded. More...

int	numberOfSequences = 0
	Number of sequences present on the alignment. More...

int	originalNumberOfResidues = 0
	Number of residues the alignment had when it was loaded. More...

int	numberOfResidues = 0
	Number of residues present on the alignment if it is aligned. More...

bool	isAligned = false
	Flag that indicates if all sequences on the alignment have the same length (Including gaps). More...

std::string *	sequences = nullptr
	Vector containing the sequences. More...

std::string *	seqsName = nullptr
	String vector containing the sequences names. More...

std::string *	seqsInfo = nullptr
	Vector containing extra information about each sequence. More...

std::string	filename
	Filename where this alignment was loaded from. More...

std::string	alignmentInfo
	String containing information of the alignment as a whole. More...

float **	identities = nullptr
	2D Matrix that represents how much each sequence resembles other sequences in the same MSA More...

float **	overlaps = nullptr
	Matrix that stores the overlap between sequences of an alignment. See Alignment::calculateSeqOverlap. More...

int *	saveResidues = nullptr
	Vector containing which residues will be kept/removed. -1 Indicates a 'removed/toRemove'. Otherwise residue/column will be kept. More...

int *	saveSequences = nullptr
	Vector containing which sequences will be kept/removed. -1 Indicates a 'removed/toRemove'. Otherwise sequence will be kept. More...

Private Attributes
int	dataType = SequenceTypes::NotDefined
	Flag variable that represents the type of the alignment. More...

Detailed Description

Class containing an alignment
This class stores the alignment sequences with it's names, residues and extra information.
It contains multiple methods regarding the sequences.
It also contains submodules that provide methods for Calculating statistics, Trim the alignment and Printing sequences information.

Definition at line 49 of file Alignment.h.

Constructor & Destructor Documentation

◆ Alignment() [1/2]

Alignment::Alignment ( void )

Constructor.

Definition at line 46 of file Alignment.cpp.

References Cleaner::Cleaner(), Cleaning, dataType, identities, isAligned, statistics::Manager::Manager(), NotDefined, numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, saveResidues, saveSequences, SeqRef, seqsInfo, seqsName, sequences, SequencesMatrix, and Statistics.

Referenced by getTranslationCDS(), and FormatHandling::FormatManager::splitAlignmentKeeping().

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◆ Alignment() [2/2]

Alignment::Alignment ( Alignment & originalAlignment )

Copy Constructor.
The copy constructor does not make a copy of all structures present on the original alignment.
Instead, all alignments that share a common origin, share some information, and also, a counter (Alignment::SeqRef) of how many alignments share the same information.
This allows us to keep the information on memory while any alignment is using it.
When an alignment is destroyed, the counter is substracted by 1, and, if it is 0 after the substraction, the shared data is destroyed.

Definition at line 87 of file Alignment.cpp.

References alignmentInfo, Cleaner::Cleaner(), Cleaning, dataType, filename, identities, isAligned, statistics::Manager::Manager(), numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, saveResidues, saveSequences, SeqRef, seqsInfo, seqsName, sequences, SequencesMatrix, and Statistics.

Referenced by Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanOverlapSeq(), Cleaner::cleanStrict(), Cleaner::getClustering(), statistics::Consistency::perform(), Cleaner::removeColumns(), and Cleaner::removeSequences().

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◆ ~Alignment()

Alignment::~Alignment ( void )

Destructor. The destructor takes care of removing the non-shared information of each alignment when is destroyed.
It also substracts 1 from the shared counter Alignment::SeqRef.
When Alignment::SeqRef arrives to 0, the shared data is destroyed, including Alignment::SeqRef.

Definition at line 134 of file Alignment.cpp.

References Cleaning, identities, numberOfSequences, saveResidues, saveSequences, SeqRef, seqsInfo, seqsName, sequences, SequencesMatrix, and Statistics.

Member Function Documentation

◆ alignmentSummaryHTML()

Alignment::alignmentSummaryHTML	(	const Alignment &	trimmedAlig,
		const char *const	destFile
	)

Method to report the trimming results in HTML.
Outputs an HTML file that shows visually what has been done to the alignment (removed sequences or residues) and the stats used to do so.

Parameters

trimmedAlig	Trimmed alignment to compare with.
destFile	Filename where to save the results.

Returns: True if correct.
False if file couldn't be open or alignment is not aligned.

Definition at line 1167 of file Alignment.cpp.

References statistics::Manager::consistency, debug, utils::determineColor(), filename, statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), statistics::Similarity::getMdkWindowedVector(), statistics::Consistency::getValues(), isAligned, utils::max(), NotAligned, numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, reporting::reportManager::report(), saveResidues, saveSequences, seqsName, sequences, statistics::Manager::similarity, and Statistics.

Referenced by trimAlManager::output_reports().

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◆ alignmentSummarySVG()

Alignment::alignmentSummarySVG	(	Alignment &	trimmedAlig,
		const char *	destFile,
		int	blocks
	)

Method to report the trimming results in SVG.
Outputs a SVG file that shows visually what has been done to the alignment (removed sequences or residues) and the stats used to do so.

Parameters

trimmedAlig	Trimmed alignment obtained from the object calling this function.
destFile	Filename where to save the results.
blocks	Size in residues to report. 120 by default.

Returns: True if everything went ok.
False if file couldn't be open or alignment is not aligned.

Definition at line 1708 of file Alignment.cpp.

References statistics::Manager::consistency, debug, utils::determineColor(), filename, statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), statistics::Similarity::getMdkWindowedVector(), statistics::Consistency::getValues(), isAligned, utils::max(), NotAligned, numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, reporting::reportManager::report(), saveResidues, saveSequences, seqsName, sequences, statistics::Manager::similarity, and Statistics.

Referenced by trimAlManager::output_reports().

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◆ calculateColIdentity()

Alignment::calculateColIdentity ( float * columnIdentity )

Method that calculates the columns identity value.
This is, the frequency of the most present element in the column, being residue, indetermination and gap allowed.

Parameters

[out] columnIdentity Vector to fill with identities for each column.

Definition at line 1074 of file Alignment.cpp.

References AA, getAlignmentType(), numberOfResidues, numberOfSequences, and sequences.

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◆ calculateSeqOverlap()

Alignment::calculateSeqOverlap ( )

Calculates overlap between sequences.

Definition at line 378 of file Alignment.cpp.

References AA, getAlignmentType(), numberOfResidues, numberOfSequences, overlaps, and sequences.

Referenced by printSeqOverlap().

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◆ checkCorrespondence()

Alignment::checkCorrespondence	(	std::string *	names,
		int *	lenghts,
		int	totalInputSequences,
		int	multiple = `1`
	)

Function to check CDS file.
.

It checks if sequences of input alignment are all present on the CDS file.
If nucleotide sequence is larger than protein sequence length * 3, warns about it and cuts the nucleotide sequence
If sequence has indetermination symbols, it warns about it.

If nucleotide sequence is smaller than protein sequence * 3, it adds some 'N' at the end of the nucleotide sequence.

Parameters

names	Vector containing the names to check.
lenghts	Vector containing the length of each sequence.
totalInputSequences	Number of sequences present.
multiple	Multiplies the length of each sequence by this number.

Returns: True if all went right.
False if there is a sequence in the alignment but not in the names vector.

Definition at line 716 of file Alignment.cpp.

References debug, IncludingIndeterminationSymbols, LessNucleotidesThanExpected, utils::min(), numberOfSequences, utils::removeCharacter(), reporting::reportManager::report(), seqsName, SequenceNotPresentInCDS, sequences, and SequenceWillBeCut.

Referenced by trimAlManager::check_backtranslation_infile_names_correspondence().

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◆ fillMatrices()

Alignment::fillMatrices	(	bool	aligned,
		bool	checkInvalidChars = `true`
	)

Method to initialize matrices and check if the sequences have been correctly loaded and are free of errors
It checks if sequences contain unknown characters, sets the isAligned flag and initializes 'saveResidues' and 'saveSequences', depending on the sizes of the sequences (whether or not they have the same length).

Parameters

aligned Flag to make the method check if the alignment is aligned or not.

Note: Even with the aligned flag set to false, if the alignment is aligned it will initialize the variables 'saveResidues' and 'saveSequences', allowing the alignment to be trimmed.

Returns: True if the alignment information was ok.
False if there was a problem.
This could happen if the sequences contain any unknown character or if aligned flag is set up to true and the sequences have variable sizes.

Definition at line 794 of file Alignment.cpp.

References debug, filename, isAligned, NotAligned, numberOfResidues, numberOfSequences, reporting::reportManager::report(), saveResidues, saveSequences, seqsName, sequences, SequencesNotSameSize, and UnknownCharacter.

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◆ getAlignmentType()

Alignment::getAlignmentType ( void ) const

Alignment type getter.
See SequenceTypes.

Returns: Int representing the alignment type.

Definition at line 469 of file Alignment.cpp.

References utils::checkAlignmentType(), dataType, NotDefined, numberOfResidues, numberOfSequences, and sequences.

Referenced by calculateColIdentity(), statistics::Similarity::calculateMatrixIdentity(), Cleaner::calculateSeqIdentity(), calculateSeqOverlap(), Cleaner::calculateSpuriousVector(), statistics::Similarity::calculateVectors(), trimAlManager::check_coding_sequences_type(), trimAlManager::create_or_use_similarity_matrix(), main(), statistics::Consistency::perform(), and prepareCodingSequence().

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◆ getNumAminos()

Alignment::getNumAminos ( void )

Residues number getter. It counts gaps as residue.

Returns: Number of residues in the alignment.

Definition at line 252 of file Alignment.cpp.

References numberOfResidues.

Referenced by trimAlManager::check_block_size(), trimAlManager::CleanResiduesNonAuto(), statistics::Consistency::compareAndChoose(), statistics::Consistency::forceComparison(), and statistics::Consistency::perform().

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◆ getNumSpecies()

Alignment::getNumSpecies ( void )

Number of sequences getter.

Returns: Number of sequences in the alignment.

Definition at line 245 of file Alignment.cpp.

References numberOfSequences.

Referenced by trimAlManager::check_backtranslation_infile_names_correspondence(), trimAlManager::check_clusters_incompatibilities(), statistics::Consistency::compareAndChoose(), statistics::Consistency::forceComparison(), and prepareCodingSequence().

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◆ getSequenceNameOrder()

Alignment::getSequenceNameOrder	(	std::string *	names,
		int *	orderVector
	)

Method to map two sets of sequences, own and external.
The method accepts a vector of names, and test them against the alignment own sequences' names.
If the sequence is present, its index will be stored in orderVector.
.

Parameters

	names	Vector of sequences names to map.
[out]	orderVector	Vector of orders to fill.

Returns: True if both sets have the same sequences.
False otherwise.

Definition at line 445 of file Alignment.cpp.

References numberOfSequences, and seqsName.

Referenced by statistics::Consistency::compareAndChoose(), and statistics::Consistency::forceComparison().

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◆ getSequences() [1/3]

Alignment::getSequences ( std::string * names )

Getter for the sequences names.

Parameters

[out] names Vector of sequences names to fill.

Definition at line 416 of file Alignment.cpp.

References numberOfSequences, and seqsName.

Referenced by statistics::Consistency::compareAndChoose(), and statistics::Consistency::forceComparison().

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◆ getSequences() [2/3]

Alignment::getSequences	(	std::string *	names,
		int *	lenghts
	)

Getter for the sequences names and its lenghts.

Parameters

[out]	names	Vector of sequences names to fill.
[out]	lenghts	Vector of lenghts to fill.

Definition at line 424 of file Alignment.cpp.

References numberOfSequences, utils::removeCharacter(), seqsName, and sequences.

Referenced by trimAlManager::check_backtranslation_infile_names_correspondence().

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◆ getSequences() [3/3]

Alignment::getSequences	(	std::string *	names,
		std::string *	sequences,
		int *	lenghts
	)

Getter for the sequences, its names and lenghts.

Parameters

[out]	names	Vector of sequences names to fill.
[out]	sequences	Vector of sequences to fill.
[out]	lenghts	Vector of lenghts to fill.

Definition at line 434 of file Alignment.cpp.

References numberOfSequences, utils::removeCharacter(), seqsName, and sequences.

Referenced by prepareCodingSequence().

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◆ getTranslationCDS()

Alignment::getTranslationCDS ( Alignment * proteinAlignment )

Method to back translate a protein alignment using the sequences present on the current alignment.
Current alignment should contain the original sequences which were translated to protein sequences, without any gap.

Note: It's recommended to translate from dna to protein and then, align the protein sequences.

Parameters

proteinAlignment Protein Alignment to use as origin.

Returns: Pointer to new alignment.

Definition at line 169 of file Alignment.cpp.

References Alignment(), numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, saveResidues, saveSequences, seqsInfo, seqsName, and sequences.

Referenced by trimAlManager::postprocess_alignment().

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◆ isFileAligned()

Alignment::isFileAligned ( void )

isAligned getter.

Returns: Whether the alignment is aligned or not.

Definition at line 495 of file Alignment.cpp.

References isAligned.

Referenced by trimAlManager::check_backtranslations(), trimAlManager::check_file_aligned(), trimAlManager::clean_alignment(), statistics::Consistency::perform(), and printAlignmentInfo().

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◆ prepareCodingSequence()

Alignment::prepareCodingSequence	(	bool	splitByStopCodon,
		bool	ignoreStopCodon,
		Alignment *	proteinAlignment
	)

Method to check if the CDS file is correct.
Based on nature of residues: DNA/RNA (Most of the residues)
There is no gaps on the whole dataset.
Each sequence is a multiple of 3.

It will also remove or split stop codons depending on the flags passed.

Parameters

splitByStopCodon	Flag that informs the method to split sequences if it finds any stop codon.
ignoreStopCodon	Flag that informs the method to stop reading sequence if it finds any stop codon.
proteinAlignment	Alignment containing protein sequences which names contains all names in the current alignment.

Definition at line 528 of file Alignment.cpp.

References AA, CDScontainsProteinSequences, CuttingSequence, debug, getAlignmentType(), getNumSpecies(), getSequences(), numberOfSequences, reporting::reportManager::report(), seqsName, SequenceContainsGap, SequenceHasStopCodon, SequenceNotMultipleOfThree, and sequences.

Referenced by trimAlManager::check_and_prepare_coding_sequence().

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◆ printAlignmentInfo()

Alignment::printAlignmentInfo ( std::ostream & output )

Print information about sequences number, average sequence length, maximum and minimum sequences length, etc.

Parameters

output Output stream.

Definition at line 868 of file Alignment.cpp.

References isFileAligned(), numberOfResidues, numberOfSequences, seqsName, and sequences.

Referenced by main().

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◆ printSeqIdentity()

Alignment::printSeqIdentity ( void )

Method to print different identity values computed from the alignment.
In this method we assess the identity values matrix, as well as different average values.
Moreover, the method computes which one is the most similar sequence.

Definition at line 912 of file Alignment.cpp.

References Cleaner::calculateSeqIdentity(), Cleaning, identities, utils::max(), numberOfSequences, originalNumberOfSequences, and seqsName.

Referenced by trimAlManager::print_statistics().

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◆ printSeqOverlap()

Alignment::printSeqOverlap ( void )

Prints the overlap between sequences.

Definition at line 1001 of file Alignment.cpp.

References calculateSeqOverlap(), utils::max(), numberOfSequences, overlaps, and seqsName.

Referenced by trimAlManager::print_statistics().

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◆ setBlockSize()

Alignment::setBlockSize ( int blockSize )

BlockSize Setter.

Parameters

blockSize New value.

Definition at line 267 of file Alignment.cpp.

References Cleaner::blockSize, and Cleaning.

Referenced by trimAlManager::innerPerform().

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◆ setKeepSequencesFlag()

Alignment::setKeepSequencesFlag ( bool newFlagValue )

Keep Sequences setter.

Parameters

newFlagValue New flag value

Definition at line 274 of file Alignment.cpp.

References Cleaning, and Cleaner::keepSequences.

Referenced by trimAlManager::innerPerform().

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◆ setWindowsSize()

Alignment::setWindowsSize	(	int	ghWindow,
		int	shWindow
	)

Windows setter.

Parameters

ghWindow	Half the Gap Window.
shWindow	Half the Similarity Window.

Definition at line 259 of file Alignment.cpp.

References statistics::Manager::ghWindow, statistics::Manager::shWindow, and Statistics.

Referenced by trimAlManager::set_window_size().

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◆ statSVG()

bool Alignment::statSVG ( const char *const destFile )

Definition at line 1431 of file Alignment.cpp.

References statistics::Manager::consistency, filename, statistics::Manager::gaps, statistics::Gaps::getGapsWindow(), statistics::Similarity::getMdkWindowedVector(), statistics::Consistency::getValues(), numberOfResidues, originalNumberOfResidues, originalNumberOfSequences, utils::quicksort(), statistics::Manager::similarity, and Statistics.

Referenced by trimAlManager::svg_stats_out().

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◆ updateSequencesAndResiduesNums()

Alignment::updateSequencesAndResiduesNums	(	bool	countSequences = `true`,
		bool	countResidues = `true`
	)

Updates the sequence number and residue number based on saveResidues and saveSequences.

Parameters

countSequences	Whether to count sequences
countResidues	Whether to count residues

Definition at line 2347 of file Alignment.cpp.

References numberOfResidues, numberOfSequences, originalNumberOfResidues, originalNumberOfSequences, saveResidues, and saveSequences.

Referenced by Cleaner::removeColumns(), Cleaner::removeOnlyTerminal(), and Cleaner::removeSequences().

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Member Data Documentation

◆ alignmentInfo

Alignment::alignmentInfo

String containing information of the alignment as a whole.

Definition at line 86 of file Alignment.h.

Referenced by Alignment().

◆ Cleaning

Alignment::Cleaning = nullptr

Trimming submodule.
It contains methods and variables related to trimming.

Definition at line 58 of file Alignment.h.

Referenced by Alignment(), Cleaner::calculateRepresentativeSeq(), Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanOverlapSeq(), trimAlManager::CleanResiduesAuto(), trimAlManager::CleanResiduesNonAuto(), trimAlManager::CleanSequences(), Cleaner::cleanStrict(), trimAlManager::innerPerform(), trimAlManager::postprocess_alignment(), printSeqIdentity(), Cleaner::removeColumns(), Cleaner::removeSequences(), setBlockSize(), setKeepSequencesFlag(), and ~Alignment().

◆ dataType

Alignment::dataType = SequenceTypes::NotDefined

private

Flag variable that represents the type of the alignment.

Definition at line 51 of file Alignment.h.

Referenced by Alignment(), and getAlignmentType().

◆ filename

Alignment::filename

Filename where this alignment was loaded from.

Definition at line 84 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), fillMatrices(), trimAlManager::output_reports(), trimAlManager::perform(), statistics::Mold::printAccumulative(), statistics::Mold::printByColumn(), statistics::Similarity::printConservationAcl(), statistics::Similarity::printConservationColumns(), statistics::Gaps::printGapsAcl(), statistics::Gaps::printGapsColumns(), statistics::Consistency::printStatisticsFileAcl(), statistics::Consistency::printStatisticsFileColumns(), FormatHandling::FormatManager::replaceINtag(), FormatHandling::FormatManager::splitAlignmentKeeping(), and statSVG().

◆ identities

Alignment::identities = nullptr

2D Matrix that represents how much each sequence resembles other sequences in the same MSA

Identity score between two sequences is the ratio of identical residues by the total length (common and no-common residues) among them.

Definition at line 89 of file Alignment.h.

Referenced by Alignment(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateRepresentativeSeq(), Cleaner::calculateSeqIdentity(), Cleaner::getCutPointClusters(), printSeqIdentity(), Cleaner::selectMethod(), and ~Alignment().

◆ isAligned

Alignment::isAligned = false

Flag that indicates if all sequences on the alignment have the same length (Including gaps).

Definition at line 76 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), fillMatrices(), isFileAligned(), and main().

◆ numberOfResidues

Alignment::numberOfResidues = 0

Number of residues present on the alignment if it is aligned.

Definition at line 74 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), calculateColIdentity(), Cleaner::calculateSeqIdentity(), calculateSeqOverlap(), statistics::Similarity::calculateVectors(), trimAlManager::check_select_cols_and_seqs_incompatibilities(), Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanStrict(), Cleaner::computeComplementaryAlig(), fillMatrices(), getAlignmentType(), getNumAminos(), getTranslationCDS(), printAlignmentInfo(), statistics::Consistency::printStatisticsFileAcl(), statistics::Consistency::printStatisticsFileColumns(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeSmallerBlocks(), FormatHandling::FormatManager::saveAlignments(), FormatHandling::FormatManager::splitAlignmentKeeping(), statSVG(), and updateSequencesAndResiduesNums().

◆ numberOfSequences

Alignment::numberOfSequences = 0

Number of sequences present on the alignment.

Definition at line 70 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), statistics::Gaps::calcCutPoint(), statistics::Gaps::calcCutPoint2ndSlope(), calculateColIdentity(), calculateSeqOverlap(), trimAlManager::check_select_cols_and_seqs_incompatibilities(), checkCorrespondence(), Cleaner::computeComplementaryAlig(), fillMatrices(), getAlignmentType(), Cleaner::getClustering(), Cleaner::getCutPointClusters(), getNumSpecies(), getSequenceNameOrder(), getSequences(), getTranslationCDS(), prepareCodingSequence(), printAlignmentInfo(), printSeqIdentity(), printSeqOverlap(), Cleaner::removeAllGapsSeqsAndCols(), FormatHandling::FormatManager::saveAlignments(), Cleaner::selectMethod(), FormatHandling::FormatManager::splitAlignmentKeeping(), updateSequencesAndResiduesNums(), ~Alignment(), and statistics::Similarity::~Similarity().

◆ originalNumberOfResidues

Alignment::originalNumberOfResidues = 0

Number of residues the alignment had when it was loaded.

Definition at line 72 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), statistics::Gaps::applyWindow(), statistics::Similarity::applyWindow(), statistics::Gaps::calcCutPoint(), statistics::Similarity::calcCutPoint(), statistics::Gaps::calcCutPoint2ndSlope(), statistics::Gaps::calcCutPointMixSlope(), statistics::Similarity::calculateMatrixIdentity(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateSpuriousVector(), statistics::Similarity::calculateVectors(), statistics::Gaps::CalculateVectors(), Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanCombMethods(), Cleaner::cleanCompareFile(), Cleaner::cleanStrict(), Cleaner::computeComplementaryAlig(), statistics::Gaps::Gaps(), getTranslationCDS(), statistics::Consistency::perform(), statistics::Mold::printAccumulative(), statistics::Mold::printByColumn(), statistics::Similarity::printConservationAcl(), statistics::Similarity::printConservationColumns(), statistics::Manager::printCorrespondence(), statistics::Gaps::printGapsAcl(), statistics::Gaps::printGapsColumns(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeOnlyTerminal(), Alignment::sequencesMatrix::sequencesMatrix(), statistics::Similarity::Similarity(), FormatHandling::FormatManager::splitAlignmentKeeping(), statSVG(), and updateSequencesAndResiduesNums().

◆ originalNumberOfSequences

Alignment::originalNumberOfSequences = 0

Number of sequences the alignment had when it was loaded.

Definition at line 68 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), statistics::Gaps::applyWindow(), statistics::Gaps::calcCutPoint(), statistics::Gaps::calcCutPointMixSlope(), statistics::Similarity::calculateMatrixIdentity(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateRepresentativeSeq(), Cleaner::calculateSeqIdentity(), Cleaner::calculateSpuriousVector(), statistics::Similarity::calculateVectors(), statistics::Gaps::CalculateVectors(), trimAlManager::check_absolute_gap_theshold(), Cleaner::cleanNoAllGaps(), Cleaner::cleanOverlapSeq(), Cleaner::cleanSpuriousSeq(), Cleaner::computeComplementaryAlig(), statistics::Gaps::Gaps(), Cleaner::getClustering(), Cleaner::getCutPointClusters(), getTranslationCDS(), trimAlManager::perform(), statistics::Gaps::printGapsAcl(), statistics::Gaps::printGapsColumns(), printSeqIdentity(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeDuplicates(), Alignment::sequencesMatrix::sequencesMatrix(), FormatHandling::FormatManager::splitAlignmentKeeping(), statSVG(), and updateSequencesAndResiduesNums().

◆ overlaps

Alignment::overlaps = nullptr

Matrix that stores the overlap between sequences of an alignment. See Alignment::calculateSeqOverlap.

Definition at line 92 of file Alignment.h.

Referenced by calculateSeqOverlap(), and printSeqOverlap().

◆ saveResidues

Alignment::saveResidues = nullptr

Vector containing which residues will be kept/removed.
-1 Indicates a 'removed/toRemove'. Otherwise residue/column will be kept.

Definition at line 95 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateSeqIdentity(), Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanCombMethods(), Cleaner::cleanStrict(), Cleaner::computeComplementaryAlig(), fillMatrices(), getTranslationCDS(), statistics::Manager::printCorrespondence(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeColumns(), Cleaner::removeOnlyTerminal(), Cleaner::removeSmallerBlocks(), updateSequencesAndResiduesNums(), and ~Alignment().

◆ saveSequences

Alignment::saveSequences = nullptr

Vector containing which sequences will be kept/removed.
-1 Indicates a 'removed/toRemove'. Otherwise sequence will be kept.

Definition at line 96 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateRepresentativeSeq(), Cleaner::calculateSeqIdentity(), statistics::Gaps::CalculateVectors(), Cleaner::cleanOverlapSeq(), Cleaner::computeComplementaryAlig(), fillMatrices(), Cleaner::getClustering(), Cleaner::getCutPointClusters(), getTranslationCDS(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeDuplicates(), Cleaner::removeSequences(), updateSequencesAndResiduesNums(), and ~Alignment().

◆ SeqRef

Alignment::SeqRef = nullptr

Pointer to keep a count of how many alignments depend on the same shared-sequences.
Increased on each trim step, and automatically reduced on each alignment destroy.
If it arrives to 0, the last alignment being destroyed will also take care of releasing memory for shared information.

Definition at line 66 of file Alignment.h.

Referenced by Alignment(), and ~Alignment().

◆ seqsInfo

Alignment::seqsInfo = nullptr

Vector containing extra information about each sequence.

Definition at line 82 of file Alignment.h.

Referenced by Alignment(), getTranslationCDS(), and ~Alignment().

◆ seqsName

Alignment::seqsName = nullptr

String vector containing the sequences names.

Definition at line 80 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), checkCorrespondence(), fillMatrices(), getSequenceNameOrder(), getSequences(), getTranslationCDS(), trimAlManager::perform(), prepareCodingSequence(), printAlignmentInfo(), printSeqIdentity(), printSeqOverlap(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeDuplicates(), Alignment::sequencesMatrix::sequencesMatrix(), FormatHandling::FormatManager::splitAlignmentKeeping(), and ~Alignment().

◆ sequences

Alignment::sequences = nullptr

Vector containing the sequences.

Definition at line 78 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), calculateColIdentity(), statistics::Manager::calculateGapStats(), statistics::Similarity::calculateMatrixIdentity(), Cleaner::calculateRelaxedSeqIdentity(), Cleaner::calculateRepresentativeSeq(), Cleaner::calculateSeqIdentity(), calculateSeqOverlap(), Cleaner::calculateSpuriousVector(), statistics::Similarity::calculateVectors(), statistics::Gaps::CalculateVectors(), checkCorrespondence(), fillMatrices(), getAlignmentType(), Cleaner::getCutPointClusters(), getSequences(), getTranslationCDS(), prepareCodingSequence(), printAlignmentInfo(), Cleaner::removeAllGapsSeqsAndCols(), Cleaner::removeDuplicates(), Alignment::sequencesMatrix::sequencesMatrix(), FormatHandling::FormatManager::splitAlignmentKeeping(), and ~Alignment().

◆ SequencesMatrix

Alignment::SequencesMatrix = nullptr

SequencesMatrix submodule
This helper module stores the sequences without gaps. Useful when comparing MSA.

Definition at line 62 of file Alignment.h.

Referenced by Alignment(), statistics::Consistency::compareAndChoose(), statistics::Consistency::forceComparison(), statistics::Consistency::perform(), and ~Alignment().

◆ Statistics

Alignment::Statistics = nullptr

Statistics submodule.
It contains methods and variables related to statistics calculation and reporting.

Definition at line 60 of file Alignment.h.

Referenced by Alignment(), alignmentSummaryHTML(), alignmentSummarySVG(), statistics::Manager::calculateConservationStats(), statistics::Similarity::calculateVectors(), Cleaner::clean(), Cleaner::clean2ndSlope(), Cleaner::cleanCombMethods(), Cleaner::cleanConservation(), Cleaner::cleanGaps(), Cleaner::cleanNoAllGaps(), trimAlManager::CleanResiduesNonAuto(), trimAlManager::CleanSequences(), trimAlManager::create_or_use_similarity_matrix(), trimAlManager::innerPerform(), statistics::Consistency::perform(), trimAlManager::print_statistics(), statistics::Manager::printStatisticsConservationColumns(), statistics::Manager::printStatisticsConservationTotal(), statistics::Manager::printStatisticsGapsColumns(), statistics::Manager::printStatisticsGapsTotal(), Cleaner::removeOnlyTerminal(), statistics::Manager::setSimilarityMatrix(), setWindowsSize(), statSVG(), and ~Alignment().

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

/home/vfernandez/git/MyFork/include/Alignment/Alignment.h
/home/vfernandez/git/MyFork/source/Alignment/Alignment.cpp
/home/vfernandez/git/MyFork/Documentation/ClassDocumentation/Alignment.dox

Classes

Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Alignment() [1/2]

◆ Alignment() [2/2]

◆ ~Alignment()

Member Function Documentation

◆ alignmentSummaryHTML()

◆ alignmentSummarySVG()

◆ calculateColIdentity()

◆ calculateSeqOverlap()

◆ checkCorrespondence()

◆ fillMatrices()

◆ getAlignmentType()

◆ getNumAminos()

◆ getNumSpecies()

◆ getSequenceNameOrder()

◆ getSequences() [1/3]

◆ getSequences() [2/3]

◆ getSequences() [3/3]

◆ getTranslationCDS()

◆ isFileAligned()

◆ prepareCodingSequence()

◆ printAlignmentInfo()

◆ printSeqIdentity()

◆ printSeqOverlap()

◆ setBlockSize()

◆ setKeepSequencesFlag()

◆ setWindowsSize()

◆ statSVG()

◆ updateSequencesAndResiduesNums()

Member Data Documentation

◆ alignmentInfo

◆ Cleaning

◆ dataType

◆ filename

◆ identities

◆ isAligned

◆ numberOfResidues

◆ numberOfSequences

◆ originalNumberOfResidues

◆ originalNumberOfSequences

◆ overlaps

◆ saveResidues

◆ saveSequences

◆ SeqRef

◆ seqsInfo

◆ seqsName

◆ sequences

◆ SequencesMatrix

◆ Statistics