Main class of trimAl.
It is strutured to work with 3 calls: More...

#include <trimalManager.h>

Classes
struct	access_by

Public Types
enum	argumentReport { NotRecognized = 0, Recognized = 1, Errored = 2, Final = 3 }

Public Member Functions
	trimAlManager ()

	~trimAlManager ()

int	perform ()
	Method to perform the analysis if all checks have passed. More...

void	delete_variables ()
	Method to delete all variables that need to be deallocated. More...

FormatHandling::FormatManager &	getFormatManager ()

Public Attributes
std::vector< std::string > *	vcfs = nullptr

bool	appearErrors = false
	Flag to trace errors. More...

bool	getComplementary = false
	Flag to return the complementary alignment. More...

bool	getComplementarySeq = false

bool	columnNumbering = false
	Flag to return column numbering in report. More...

bool	nogaps = false
	Flag to use the nogaps option. More...

bool	noallgaps = false
	Flag to use the noallgaps option. More...

bool	gappyout = false
	Flag to use the gappyout trimming method. More...

bool	strict = false
	Flag to use the strict trimming method. More...

bool	strictplus = false
	Flag to use the strictplus trimming method. More...

bool	automated1 = false
	Flag to use the automated1 trimming method. More...

bool	sgc = false
	Flag to show the Gaps Scores per column. More...

bool	sgt = false
	Flag to show the Accumulated Gaps Scores. More...

bool	ssc = false
	Flag to show the Similarity Scores per column. More...

bool	sst = false
	Flag to show the Accumulated Similarity Scores. More...

bool	sfc = false
	Flag to show the Sum of Pairs scores per column. More...

bool	sft = false
	Flag to show the Accumulated Sum of Pairs. More...

bool	sident = false
	Flag to show identity scores in the alignment. More...

bool	soverlap = false
	Flag to show overlap scores in the alignment. More...

bool	selectSeqs = false
	Flag to select sequences manually from the alignment. More...

bool	selectCols = false
	Flag to select columns manually from the alignment. More...

bool	splitByStopCodon = false
	Flag to use the SplitByCodonStop option. More...

bool	terminalOnly = false
	Flag to use the Terminal Only option. More...

bool	keepSeqs = false
	Flag to keep sequences in the alignment. More...

bool	ignoreStopCodon = false
	Flag to use the Ignore Stop Codon option. More...

bool	ignoreFilter = false

bool	removeDuplicates = false

float	conservationThreshold = -1
	Similarity Threshold to use while trimming. More...

float	gapThreshold = -1
	Gap Threshold to use while trimming. More...

float	similarityThreshold = -1
	Similarity Threshold to use while trimming. More...

float	consistencyThreshold = -1
	Consistency Threshold to use while trimming. More...

float	residuesOverlap = -1
	Residues Overlap to use while trimming. More...

float	sequenceOverlap = -1
	Sequence Overlap to use while trimming. More...

float	maxIdentity = -1
	Max Identity to use while trimming. More...

float	minCoverage = -1

float	minQuality = -1

int	i = 1
	Argument Iterator Variable. More...

int	stats = 0
	Stats Flag to use in reporting. For each stat requested, this flag is decreased by one. More...

int	windowSize = -1
	Window Size to use while trimming. More...

int	gapWindow = -1
	Gap Window Size to use while trimming. More...

int	similarityWindow = -1
	Similarity Window to use while trimming. More...

int	consistencyWindow = -1
	Consistency Window to use while trimming. More...

int	blockSize = -1
	Block Size to use while trimming. More...

int	clusters = -1
	Number of most representative sequences we are going to use. More...

int	automatedMethodCount = -1
	Integer counter of the automatic methods. If the counter is bigger than 0, we are using an automatic method. If the counter is bigger than 1, we are trying to use multiple automatic methods. More...

int	alternative_matrix = -1
	Int that represents which alternative matrix to use, where '-1' means no alternative matrix, and '1' means degenerated_nt_identity. More...

int	gapAbsoluteThreshold = -1

int *	delColumns = nullptr
	Vector that contains the column indexes the user specified to be removed. More...

int *	delSequences = nullptr
	Vector that contains the sequence indexes the user specified to be removed. More...

int *	sequencesLengths = nullptr
	Vector that contains the sequences lengths of each sequence in the backtranslation option. More...

size_t	argumentLength = size_t(-1)
	Temp variable to use when there is a need to copy an argument to a char array. More...

std::string *	sequencesNames = nullptr
	Temporal variable to use in backtranslation option to compare with infile. More...

std::ifstream	compare
	Temporal variable to open files in trimAlManager::check_multiple_files_comparison function. More...

statistics::similarityMatrix *	similMatrix = nullptr
	Temporal Similarity Matrix. More...

Alignment *	origAlig = nullptr
	Main alignment used/loaded on trimAl in combination with singleAlig. More...

Alignment *	singleAlig = nullptr
	Alignment obtained by making modifications to singleAlig or backtranslationAlig. More...

Alignment *	tempAlig = nullptr
	Temporal alignment that allows us to make some changes to trimAlManager::singleAlig, destroy it and set trimAlManager::singleAlig to this. More...

Alignment *	backtranslationAlig = nullptr
	Alignment used on the backtranslation functionality. More...

Alignment **	compareAlignmentsArray = nullptr
	Alignment Vector used on trimAlManager::check_multiple_files_comparison to compare them. More...

char	c
	Temporal char variable. More...

char *	forceFile = nullptr
	Forcefile to use in combination with multiple files comparison, to compare them against this. More...

char *	infile = nullptr
	File to load the alignment when only one alignment has trimming interest. More...

char *	backtransFile = nullptr
	File to load the alignment containing the backtranslation information. More...

char *	outfile = nullptr
	File to output the trimmed alignment. This can contain tags which will be traduced to some variables: [in] will be changed with the original filename. [format] will be changed with the output format name specified. [extension] will be changed to the correct format extension. More...

char *	htmlOutFile = nullptr
	File to output the html report. More...

char *	svgOutFile = nullptr
	File to output the svg report. More...

char *	svgStatsOutFile = nullptr
	File to output the svg graph showing the stats along the alignment. More...

char *	compareset = nullptr
	Pointer to the argument that contains the compareset file. More...

char *	matrixFile = nullptr
	File that contains a user defined similarity matrix. More...

char **	filesToCompare = nullptr
	Vector containing the files to compare in trimAlManager::check_multiple_files_comparison function. More...

char	line [256]
	Temporal variable to read lines from a file. More...

std::vector< std::string >	oformats
	Formats names we are going to output our trimmed alignment. More...

statistics::Consistency *	CS = nullptr

Private Member Functions
argumentReport	ignore_filter_argument (const int argc, char argv[], int *currentArg)

argumentReport	min_quality_argument (const int argc, char argv[], int *currentArg)

argumentReport	min_coverage_argument (const int argc, char argv[], int *currentArg)

argumentReport	remove_duplicates_argument (const int argc, char argv[], int *currentArg)

bool	check_vcf_incompatibility ()

bool	check_absolute_gap_theshold ()

void	check_thresholds_dependencies ()

int	innerPerform ()

void	output_reports ()

void	save_alignment ()

void	svg_stats_out ()

void	print_statistics ()
	Method to print statistics requested. More...

bool	create_or_use_similarity_matrix ()
	Method to create, load and use a similarity matrix, depending on alignment residue nature, if the user gave a specific similarity matrix, etc. More...

void	clean_alignment ()
	Core Method of the program. This is where almost all cleaning methods are called from. More...

void	postprocess_alignment ()

void	set_window_size ()
	Method to set correct window sizes depending on values for them given by the user. More...

void	menu ()
	Method to show the menu of the program. More...

void	examples ()
	Method to show the examples information about the program. More...

void	CleanSequences ()
	Method to trim or reduce the number of sequences in an alignment. It performs one or none of the following methods: More...

void	CleanResiduesAuto ()
	Method to trim the alignment using automatic or semi-automatic methods: More...

void	CleanResiduesNonAuto ()
	Method to trim the alignment using non automatic methods: More...

Private Attributes
FormatHandling::FormatManager	formatManager
	Read Write Machine that allows to manage formats easily. More...

Friends
struct	Catch::SectionInfo

template<uint T>
struct	access_by

Argument Parsing methods

Parameters

[in]	argc	Number of arguments in argv
[in]	*argv[]	Arguments passed to the program
[in,out]	*currentArg	Current argument being evaluated. It is passed as a pointer to allow methods to consume several argc

Returns: True if current argument (*currentArg) corresponds to the argument being checked.
False otherwise.

Access Level: All methods are inline-private except parseArguments(int argc, char *argv[])

Special Cases:

parseArguments(int argc, char *argv[])
Is the only public method in the group.
Calls the rest of methods in the group.
help_arguments(const int* argc, char* argv[], int* currentArg)
Is the only private method that doesn't accept *currentArg.
This is due it iterates over all values of argv before checking the rest of arguments.

int parseArguments (int argc, char **argv)

Method to parse arguments into usable structure in trimal. More...

void verbosity_argument (const int *argc, char *argv[])

Method to parse the verbosity argument.
This check is done before any other check.
This is due to trimAl not performing any action if any help argument has been provided.
. More...

argumentReport help_arguments (const int *argc, char **argv, int *currentArg)

Method to parse information arguments as help and menu. More...

argumentReport in_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the input file argument. More...

argumentReport vcf_argument (const int *argc, char *argv[], int *currentArg)

Method to parse vcf argument. More...

argumentReport out_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the output file pattern. More...

argumentReport html_out_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the html output file. More...

argumentReport timetracker_out_argument (const int *argc, char *argv[], int *currentArg)

Method to parse InternalBenchmarker output argument.
Need to be checked before any other argument. More...

argumentReport svg_out_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the svg output file. More...

argumentReport svg_stats_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the svg stats output file. More...

argumentReport out_format_arguments (const int *argc, char *argv[], int *currentArg)

Method to parse the output formats as -fasta -clustal or -formats [...]. More...

argumentReport matrix_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the custom matrix argument. More...

argumentReport compareset_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the comparset argument. More...

argumentReport force_select_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the force select argument. More...

argumentReport back_trans_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the backtranslation argument. More...

argumentReport gap_threshold_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the gap threshold argument. More...

argumentReport similarity_threshold_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the similarity threshold argument. More...

argumentReport consistency_threshold_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the consistency threshold argument. More...

argumentReport conservation_threshold_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the similarity threshold argument. More...

argumentReport select_cols_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the select columns argument. More...

argumentReport no_gaps_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the nogaps argument. More...

argumentReport no_all_gaps_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the noallgaps argument. More...

argumentReport keep_seqs_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the keepSeqs argument. More...

argumentReport keep_header_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the keepHeader argument. More...

argumentReport gappy_out_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the gappyout argument. More...

argumentReport strict_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the strict argument. More...

argumentReport strict_plus_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the strictplus argument. More...

argumentReport automated1_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the automated1 argument. More...

argumentReport residue_overlap_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the residue overlap argument. More...

argumentReport sequence_overlap_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the sequence overlap argument. More...

argumentReport seqs_select_argument (const int *argc, char *argv[], int *currentArg)

Method to parse que select sequences argument. More...

argumentReport max_identity_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the max identity argument. More...

argumentReport clusters_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the clusters argument. More...

argumentReport terminal_only_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the terminal only argument. More...

argumentReport window_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the Window argument. More...

argumentReport gap_window_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the Gap Window argument. More...

argumentReport similarity_window_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the Similarity Window argument. More...

argumentReport consistency_window_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the Consistency Window argument. More...

argumentReport block_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the Block Size argument. More...

argumentReport stats_arguments (const int *argc, char *argv[], int *currentArg)

Method to parse stats arguments. More...

argumentReport complementary_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the complementary argument. More...

argumentReport col_numbering_argument (const int *argc, char *argv[], int *currentArg)

Method to parse the column numbering argument. More...

argumentReport split_by_stop_codon_argument (const int *argc, char *argv[], int *currentArg)

Method to parse split by stop codon argument. More...

argumentReport ignore_stop_codon_argument (const int *argc, char *argv[], int *currentArg)

Method to parse ignore by stop codon argument. More...

Process Arguments Methods
bool	processArguments (char *argv[])
	Method to process the information obtained by trimAlManager::parseArguments It checks for argument incompatibilities and arguments dependencies. More...

bool	check_arguments_incompatibilities ()
	Method to check argument incompatibilities. Take in mind that an incompatibility is between two arguments, but only one method will check this incompatibility. If you are searching for the method that checks incompatibility between X and Y, this check may be done on check_X_incompatibilities or check_Y_incompatibilities. More...

bool	check_inFile_incompatibilities ()
	Method to check the inFile argument incompatibilities. More...

bool	check_select_cols_and_seqs_incompatibilities ()
	Method to check incompatibilities with select cols and select seqs arguments. More...

bool	check_thresholds_incompatibilities ()
	Method to check incompatibilities with manual thresholds. More...

bool	check_automated_methods_incompatibilities ()
	Method to check incompatibilities related to automated trimming methods. More...

bool	check_max_identity_incompatibilities ()
	Method to check max identity incompatibilities. More...

bool	check_clusters_incompatibilities ()
	Method to check clusters incompatibilities. More...

bool	check_windows_incompatibilities ()
	Method to check windows incompatibilities. More...

bool	check_stats_incompatibilities ()
	Method to check statistics incompatibilities. More...

bool	check_codon_behaviour_incompatibility ()
	Method to check incompatibilities related to how the algorithm should treat stop codons. More...

bool	check_combinations_among_thresholds_incompatibility ()
	As some thresholds are incompatible between them, we check their incompatibilities. More...

bool	check_automated_manual_incompatibilities ()
	Check if only one method, either automatic or manual has been asked. More...

bool	check_arguments_needs (char *argv[])
	Method that checks dependencies between arguments. Take in mind that dependencies may be between multiple arguments, so, if there is a dependency between arguments X, Y and Z, this dependency check may be on check_X, check_Y or check_Z. At the same time, is possible to find a function that checks this dependency specifically: check_X_with_Y_and_Z. More...

bool	check_force_selection ()
	Method to check dependency of force select argument. More...

bool	check_input_file_with_coding_sequences_argument ()
	Method to check dependency between custom coding sequence file and infile arguments. More...

bool	check_file_aligned ()
	Method to check if an alignment needs to be aligned depending on the methods that have been asked to perform and, if so, checks if alignment is aligned. More...

bool	check_similarity_matrix ()
	Method to check if given a similarity matrix, there is a need to use it. More...

bool	check_outputs_coincidence ()
	Method to check if both output patterns (alignment output and html report output) are the same, which would mean one of them would overwrite the other. More...

bool	check_col_numbering ()
	Method to check if column numbering makes sense based on the functionality asked. More...

bool	check_residue_and_sequence_overlap ()
	Method to check if both of them (residue overlap and sequence overlap) have been defined by the user as they have a dependency on each other. More...

bool	check_output_relevance ()
	Method to check if, being asked to give an HTML report, it makes logic, depending on the functionality asked. More...

bool	check_output_file_with_statistics ()
	Method to check if there is an output file to allow statistics to be given on terminal. More...

bool	check_block_size ()
	Method to check if the block size is bigger than allowed depending on size of alignment. More...

bool	check_backtranslations ()
	Method to check backtranslation needs. More...

bool	check_coding_sequences_type ()
	Method to check the type of sequences present in the backtranslationAlig. More...

bool	check_and_prepare_coding_sequence ()
	Method to check and prepare the coding sequence. More...

bool	check_backtranslation_infile_names_correspondence ()
	Method to check if the origAlig and backtranslationAlig are compatible in names to make the backtranslation behaviour. More...

void	check_compareset_window_argument ()
	Method to check and warn if windowsize and compareset has been given. More...

void	check_output_format ()
	Method to check if an output format has been given. If no output format has been given, it will use the inFile format. More...

bool	performCompareset ()
	Method to check if multiple files comparison has been set correctly. It also perform some calculations needed on comparfiles behaviour. More...

Detailed Description

Main class of trimAl.
It is strutured to work with 3 calls:

trimAlManager::parseArguments(int argc, char *argv[]) :
To parse the arguments passed to the program.
trimAlManager::processArguments(char* argv[]) :
To check if every argument passed in compatible with the rest, and also, if it has all it's dependencies fulfilled.
trimAlManager::perform() :
To perform the logic requested by passed arguments.

See main

Definition at line 62 of file trimalManager.h.

Member Enumeration Documentation

◆ argumentReport

enum trimAlManager::argumentReport

Enumerator
NotRecognized
Recognized
Errored
Final

Definition at line 179 of file trimalManager.h.

Constructor & Destructor Documentation

◆ trimAlManager()

trimAlManager::trimAlManager ( )

Definition at line 53 of file trimalManager.cpp.

◆ ~trimAlManager()

trimAlManager::~trimAlManager ( )

Definition at line 59 of file trimalManager.cpp.

References delete_variables().

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Member Function Documentation

◆ automated1_argument()

bool trimAlManager::automated1_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the automated1 argument.

inline

Definition at line 697 of file trimalManager.cpp.

References automated1, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ back_trans_argument()

bool trimAlManager::back_trans_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the backtranslation argument.

inline

Definition at line 501 of file trimalManager.cpp.

References AlignmentNotLoaded, appearErrors, argumentLength, backtransFile, backtranslationAlig, debug, formatManager, FormatHandling::FormatManager::loadAlignment(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ block_argument()

bool trimAlManager::block_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the Block Size argument.

inline

Definition at line 870 of file trimalManager.cpp.

References appearErrors, blockSize, BlockSizeNotRecognized, BlockSizeOutOfRange, debug, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ check_absolute_gap_theshold()

bool trimAlManager::check_absolute_gap_theshold ( )

inlineprivate

Definition at line 1308 of file trimalManager.cpp.

References AbsoluteGapThresholdBiggerThanNumberOfSequences, appearErrors, debug, gapAbsoluteThreshold, gapThreshold, origAlig, Alignment::originalNumberOfSequences, and reporting::reportManager::report().

Referenced by check_arguments_needs().

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◆ check_and_prepare_coding_sequence()

bool trimAlManager::check_and_prepare_coding_sequence ( )

private

Method to check and prepare the coding sequence.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1581 of file trimalManager.cpp.

References appearErrors, backtransFile, backtranslationAlig, ignoreStopCodon, origAlig, Alignment::prepareCodingSequence(), and splitByStopCodon.

Referenced by check_arguments_needs().

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◆ check_arguments_incompatibilities()

bool trimAlManager::check_arguments_incompatibilities ( )

private

Method to check argument incompatibilities.
Take in mind that an incompatibility is between two arguments, but only one method will check this incompatibility. If you are searching for the method that checks incompatibility between X and Y, this check may be done on check_X_incompatibilities or check_Y_incompatibilities.

inline

Returns: True if all incompatibilities checks have passed.
False otherwise

Definition at line 226 of file trimalManager.cpp.

References appearErrors, check_automated_methods_incompatibilities(), check_clusters_incompatibilities(), check_codon_behaviour_incompatibility(), check_combinations_among_thresholds_incompatibility(), check_inFile_incompatibilities(), check_max_identity_incompatibilities(), check_select_cols_and_seqs_incompatibilities(), check_stats_incompatibilities(), check_thresholds_incompatibilities(), check_vcf_incompatibility(), and check_windows_incompatibilities().

Referenced by processArguments().

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◆ check_arguments_needs()

bool trimAlManager::check_arguments_needs ( char * argv[] )

private

Method that checks dependencies between arguments.
Take in mind that dependencies may be between multiple arguments, so, if there is a dependency between arguments X, Y and Z, this dependency check may be on check_X, check_Y or check_Z.
At the same time, is possible to find a function that checks this dependency specifically: check_X_with_Y_and_Z.

inline

Parameters

argv	Arguments passed to the program

Returns: False if dependencies check has passed
True otherwise

Definition at line 1205 of file trimalManager.cpp.

References appearErrors, check_absolute_gap_theshold(), check_and_prepare_coding_sequence(), check_automated_manual_incompatibilities(), check_backtranslation_infile_names_correspondence(), check_backtranslations(), check_block_size(), check_coding_sequences_type(), check_col_numbering(), check_compareset_window_argument(), check_file_aligned(), check_force_selection(), check_input_file_with_coding_sequences_argument(), check_output_file_with_statistics(), check_output_format(), check_output_relevance(), check_outputs_coincidence(), check_residue_and_sequence_overlap(), check_similarity_matrix(), and check_thresholds_dependencies().

Referenced by processArguments().

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◆ check_automated_manual_incompatibilities()

bool trimAlManager::check_automated_manual_incompatibilities ( )

private

Check if only one method, either automatic or manual has been asked.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1283 of file trimalManager.cpp.

References appearErrors, automatedMethodCount, clusters, conservationThreshold, consistencyThreshold, debug, gapThreshold, getComplementary, maxIdentity, reporting::reportManager::report(), residuesOverlap, selectCols, selectSeqs, sequenceOverlap, similarityThreshold, terminalOnly, and TrimmingMethodNeeded.

Referenced by check_arguments_needs().

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◆ check_automated_methods_incompatibilities()

bool trimAlManager::check_automated_methods_incompatibilities ( )

private

Method to check incompatibilities related to automated trimming methods.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1128 of file trimalManager.cpp.

References appearErrors, automated1, automatedMethodCount, CombinationAmongTrimmingMethods, debug, gappyout, gapWindow, MoreThanOneAutomatedMethod, noallgaps, nogaps, reporting::reportManager::report(), similarityWindow, strict, strictplus, and windowSize.

Referenced by check_arguments_incompatibilities().

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◆ check_backtranslation_infile_names_correspondence()

bool trimAlManager::check_backtranslation_infile_names_correspondence ( )

private

Method to check if the origAlig and backtranslationAlig are compatible in names to make the backtranslation behaviour.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1600 of file trimalManager.cpp.

References appearErrors, backtransFile, backtranslationAlig, Alignment::checkCorrespondence(), Alignment::getNumSpecies(), Alignment::getSequences(), origAlig, sequencesLengths, and sequencesNames.

Referenced by check_arguments_needs().

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◆ check_backtranslations()

bool trimAlManager::check_backtranslations ( )

private

Method to check backtranslation needs.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1535 of file trimalManager.cpp.

References appearErrors, backtransFile, debug, ignoreStopCodon, Alignment::isFileAligned(), origAlig, ParemeterOnlyOnBacktranslation, ProteinAlignmentMustBeAligned, reporting::reportManager::report(), and splitByStopCodon.

Referenced by check_arguments_needs().

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◆ check_block_size()

bool trimAlManager::check_block_size ( )

private

Method to check if the block size is bigger than allowed depending on size of alignment.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1526 of file trimalManager.cpp.

References appearErrors, blockSize, BlocksizeTooBig, debug, Alignment::getNumAminos(), origAlig, and reporting::reportManager::report().

Referenced by check_arguments_needs().

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◆ check_clusters_incompatibilities()

bool trimAlManager::check_clusters_incompatibilities ( )

private

Method to check clusters incompatibilities.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1175 of file trimalManager.cpp.

References appearErrors, clusters, debug, Alignment::getNumSpecies(), MoreClustersThanSequences, origAlig, and reporting::reportManager::report().

Referenced by check_arguments_incompatibilities().

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◆ check_coding_sequences_type()

bool trimAlManager::check_coding_sequences_type ( )

private

Method to check the type of sequences present in the backtranslationAlig.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1564 of file trimalManager.cpp.

References appearErrors, BacktransAlignIsDNA, backtransFile, backtranslationAlig, debug, DNA, Alignment::getAlignmentType(), and reporting::reportManager::report().

Referenced by check_arguments_needs().

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◆ check_codon_behaviour_incompatibility()

bool trimAlManager::check_codon_behaviour_incompatibility ( )

private

Method to check incompatibilities related to how the algorithm should treat stop codons.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1232 of file trimalManager.cpp.

References appearErrors, debug, ignoreStopCodon, IncompatibleArguments, reporting::reportManager::report(), and splitByStopCodon.

Referenced by check_arguments_incompatibilities().

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◆ check_col_numbering()

bool trimAlManager::check_col_numbering ( )

private

Method to check if column numbering makes sense based on the functionality asked.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1433 of file trimalManager.cpp.

References appearErrors, automatedMethodCount, columnNumbering, conservationThreshold, consistencyThreshold, debug, gapThreshold, reporting::reportManager::report(), selectCols, selectSeqs, similarityThreshold, and TrimmingMethodNeeded.

Referenced by check_arguments_needs().

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◆ check_combinations_among_thresholds_incompatibility()

bool trimAlManager::check_combinations_among_thresholds_incompatibility ( )

private

As some thresholds are incompatible between them, we check their incompatibilities.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1241 of file trimalManager.cpp.

References appearErrors, CombinationAmongThresholdsMethods, conservationThreshold, consistencyThreshold, debug, gapThreshold, reporting::reportManager::report(), and similarityThreshold.

Referenced by check_arguments_incompatibilities().

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◆ check_compareset_window_argument()

void trimAlManager::check_compareset_window_argument ( )

private

Method to check and warn if windowsize and compareset has been given.

inline

Definition at line 1625 of file trimalManager.cpp.

References appearErrors, compareset, debug, reporting::reportManager::report(), windowSize, and WindowSizeCompareset.

Referenced by check_arguments_needs().

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◆ check_file_aligned()

bool trimAlManager::check_file_aligned ( )

private

Method to check if an alignment needs to be aligned depending on the methods that have been asked to perform and, if so, checks if alignment is aligned.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1349 of file trimalManager.cpp.

References appearErrors, automatedMethodCount, consistencyThreshold, debug, gapThreshold, infile, Alignment::isFileAligned(), NotAligned, origAlig, reporting::reportManager::report(), residuesOverlap, selectCols, selectSeqs, sequenceOverlap, similarityThreshold, stats, and vcfs.

Referenced by check_arguments_needs().

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◆ check_force_selection()

bool trimAlManager::check_force_selection ( )

private

Method to check dependency of force select argument.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1329 of file trimalManager.cpp.

References appearErrors, compareset, debug, forceFile, ForceFileWithoutCompareDataset, and reporting::reportManager::report().

Referenced by check_arguments_needs().

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◆ check_inFile_incompatibilities()

bool trimAlManager::check_inFile_incompatibilities ( )

private

Method to check the inFile argument incompatibilities.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1025 of file trimalManager.cpp.

References appearErrors, compareset, consistencyThreshold, debug, forceFile, i, IncompatibleArguments, infile, InFileComparisonStatistics, reporting::reportManager::report(), sfc, and sft.

Referenced by check_arguments_incompatibilities().

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◆ check_input_file_with_coding_sequences_argument()

bool trimAlManager::check_input_file_with_coding_sequences_argument ( )

private

Method to check dependency between custom coding sequence file and infile arguments.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1340 of file trimalManager.cpp.

References appearErrors, backtransFile, BacktranslationWithoutMainAlignment, compareset, debug, forceFile, infile, and reporting::reportManager::report().

Referenced by check_arguments_needs().

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◆ check_max_identity_incompatibilities()

bool trimAlManager::check_max_identity_incompatibilities ( )

private

Method to check max identity incompatibilities.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1161 of file trimalManager.cpp.

References appearErrors, clusters, consistencyWindow, debug, gapWindow, maxIdentity, OnlyOneSequencesSelectionMethodAllowed, reporting::reportManager::report(), similarityWindow, WindowAndArgumentIncompatibilities, and windowSize.

Referenced by check_arguments_incompatibilities().

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◆ check_output_file_with_statistics()

bool trimAlManager::check_output_file_with_statistics ( )

private

Method to check if there is an output file to allow statistics to be given on terminal.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1501 of file trimalManager.cpp.

References appearErrors, automatedMethodCount, conservationThreshold, debug, gapThreshold, outfile, OutFileNeededWhenPrintingStatistics, reporting::reportManager::report(), similarityThreshold, and stats.

Referenced by check_arguments_needs().

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◆ check_output_format()

void trimAlManager::check_output_format ( )

private

Method to check if an output format has been given. If no output format has been given, it will use the inFile format.

inline

Definition at line 1630 of file trimalManager.cpp.

References formatManager, FormatHandling::FormatManager::getFileFormatName(), infile, and oformats.

Referenced by check_arguments_needs().

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◆ check_output_relevance()

bool trimAlManager::check_output_relevance ( )

private

Method to check if, being asked to give an HTML report, it makes logic, depending on the functionality asked.

Method to check if output is coherent.
For example, it doesn't make sense to output an HTML if there is no trimming.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1472 of file trimalManager.cpp.

References appearErrors, automatedMethodCount, clusters, conservationThreshold, consistencyThreshold, debug, gapThreshold, htmlOutFile, maxIdentity, reporting::reportManager::report(), residuesOverlap, selectCols, selectSeqs, sequenceOverlap, similarityThreshold, svgOutFile, svgStatsOutFile, and TrimmingMethodNeeded.

Referenced by check_arguments_needs().

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◆ check_outputs_coincidence()

bool trimAlManager::check_outputs_coincidence ( )

private

Method to check if both output patterns (alignment output and html report output) are the same, which would mean one of them would overwrite the other.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1396 of file trimalManager.cpp.

References appearErrors, debug, htmlOutFile, outfile, reporting::reportManager::report(), SameNameOutput, svgOutFile, and svgStatsOutFile.

Referenced by check_arguments_needs().

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◆ check_residue_and_sequence_overlap()

bool trimAlManager::check_residue_and_sequence_overlap ( )

private

Method to check if both of them (residue overlap and sequence overlap) have been defined by the user as they have a dependency on each other.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1457 of file trimalManager.cpp.

References appearErrors, debug, reporting::reportManager::report(), residuesOverlap, SequenceAndResiduesOverlapMutuallyNeeded, and sequenceOverlap.

Referenced by check_arguments_needs().

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◆ check_select_cols_and_seqs_incompatibilities()

bool trimAlManager::check_select_cols_and_seqs_incompatibilities ( )

private

Method to check incompatibilities with select cols and select seqs arguments.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1044 of file trimalManager.cpp.

References appearErrors, blockSize, clusters, debug, delColumns, delSequences, IncompatibleArguments, maxIdentity, Alignment::numberOfResidues, Alignment::numberOfSequences, OnlyOneSequencesSelectionMethodAllowed, origAlig, reporting::reportManager::report(), selectCols, SelectOnlyAccepts, and selectSeqs.

Referenced by check_arguments_incompatibilities().

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◆ check_similarity_matrix()

bool trimAlManager::check_similarity_matrix ( )

private

Method to check if given a similarity matrix, there is a need to use it.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1378 of file trimalManager.cpp.

References alternative_matrix, appearErrors, automated1, compareset, consistencyWindow, debug, gapWindow, matrixFile, MatrixGivenWithNoMethodToUseIt, reporting::reportManager::report(), SimilarityMatrixNotCompatibleWindow, similarityThreshold, ssc, sst, strict, and strictplus.

Referenced by check_arguments_needs().

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◆ check_stats_incompatibilities()

bool trimAlManager::check_stats_incompatibilities ( )

private

Method to check statistics incompatibilities.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1195 of file trimalManager.cpp.

References appearErrors, columnNumbering, debug, reporting::reportManager::report(), StatisticsArgumentIncompatibilities, and stats.

Referenced by check_arguments_incompatibilities().

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◆ check_thresholds_dependencies()

void trimAlManager::check_thresholds_dependencies ( )

private

inline

Definition at line 1636 of file trimalManager.cpp.

References appearErrors, and windowSize.

Referenced by check_arguments_needs().

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◆ check_thresholds_incompatibilities()

bool trimAlManager::check_thresholds_incompatibilities ( )

private

Method to check incompatibilities with manual thresholds.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1085 of file trimalManager.cpp.

References appearErrors, automated1, automatedMethodCount, blockSize, CombinationAmongTrimmingMethods, conservationThreshold, consistencyThreshold, debug, gappyout, gapThreshold, IncompatibleArguments, noallgaps, nogaps, reporting::reportManager::report(), similarityThreshold, strict, and strictplus.

Referenced by check_arguments_incompatibilities().

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◆ check_vcf_incompatibility()

bool trimAlManager::check_vcf_incompatibility ( )

private

inline

Definition at line 1256 of file trimalManager.cpp.

References appearErrors, debug, ignoreFilter, minCoverage, minQuality, OnlyValidWithVCF, reporting::reportManager::report(), and vcfs.

Referenced by check_arguments_incompatibilities().

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◆ check_windows_incompatibilities()

bool trimAlManager::check_windows_incompatibilities ( )

private

Method to check windows incompatibilities.

inline

Returns: True if incompatibilities check has passed
False otherwise

Definition at line 1185 of file trimalManager.cpp.

References appearErrors, consistencyWindow, debug, gapWindow, GeneralAndSpecificWindows, reporting::reportManager::report(), similarityWindow, and windowSize.

Referenced by check_arguments_incompatibilities().

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◆ clean_alignment()

void trimAlManager::clean_alignment ( )

private

Core Method of the program. This is where almost all cleaning methods are called from.

inline

Definition at line 2000 of file trimalManager.cpp.

References automatedMethodCount, CleanResiduesAuto(), CleanResiduesNonAuto(), CleanSequences(), debug, infile, Alignment::isFileAligned(), NotAligned, origAlig, and reporting::reportManager::report().

Referenced by innerPerform().

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◆ CleanResiduesAuto()

void trimAlManager::CleanResiduesAuto ( )

private

Method to trim the alignment using automatic or semi-automatic methods:

inline

Automatic1
NoGaps
NoAllGaps
Gappyout
Strict
Strictplus

Definition at line 2108 of file trimalManager.cpp.

References automated1, Cleaner::clean2ndSlope(), Cleaner::cleanCombMethods(), Cleaner::cleanGaps(), Alignment::Cleaning, Cleaner::cleanNoAllGaps(), gappyout, noallgaps, nogaps, origAlig, Cleaner::selectMethod(), singleAlig, strict, strictplus, and tempAlig.

Referenced by clean_alignment().

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◆ CleanResiduesNonAuto()

void trimAlManager::CleanResiduesNonAuto ( )

private

Method to trim the alignment using non automatic methods:

inline

Delete columns
Manual thresholds: Gap, Similarity and/or Consistency

Definition at line 2145 of file trimalManager.cpp.

References appearErrors, Cleaner::clean(), Cleaner::cleanCompareFile(), Cleaner::cleanConservation(), Cleaner::cleanGaps(), Alignment::Cleaning, conservationThreshold, statistics::Manager::consistency, consistencyThreshold, debug, delColumns, gapThreshold, Alignment::getNumAminos(), statistics::Consistency::getValues(), origAlig, Cleaner::removeColumns(), reporting::reportManager::report(), SelectOnlyAccepts, similarityThreshold, singleAlig, Alignment::Statistics, and tempAlig.

Referenced by clean_alignment().

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◆ CleanSequences()

void trimAlManager::CleanSequences ( )

private

Method to trim or reduce the number of sequences in an alignment. It performs one or none of the following methods:

inline

Clusters
MaxIdentity
Delete Sequences
Sequence Overlap

When one method is applied, NoAllGaps is also applied, as these methods rely on it

Definition at line 2051 of file trimalManager.cpp.

References Alignment::Cleaning, Cleaner::cleanNoAllGaps(), Cleaner::cleanSpuriousSeq(), clusters, delSequences, statistics::Manager::gaps, Cleaner::getClustering(), Cleaner::getCutPointClusters(), maxIdentity, origAlig, removeDuplicates, Cleaner::removeDuplicates(), Cleaner::removeSequences(), residuesOverlap, sequenceOverlap, statistics::Manager::similarity, singleAlig, Alignment::Statistics, and tempAlig.

Referenced by clean_alignment().

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◆ clusters_argument()

bool trimAlManager::clusters_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the clusters argument.

inline

Definition at line 775 of file trimalManager.cpp.

References appearErrors, clusters, ClustersValueNotRecognized, ClustersValueOutOfRange, debug, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ col_numbering_argument()

bool trimAlManager::col_numbering_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the column numbering argument.

inline

Definition at line 938 of file trimalManager.cpp.

References columnNumbering, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ compareset_argument()

bool trimAlManager::compareset_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the comparset argument.

inline

Definition at line 462 of file trimalManager.cpp.

References appearErrors, compare, compareset, debug, NotRecognized, Recognized, ReferenceFileNotLoaded, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ complementary_argument()

bool trimAlManager::complementary_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the complementary argument.

inline

Definition at line 926 of file trimalManager.cpp.

References getComplementary, getComplementarySeq, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ conservation_threshold_argument()

bool trimAlManager::conservation_threshold_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the similarity threshold argument.

inline

Definition at line 597 of file trimalManager.cpp.

References appearErrors, conservationThreshold, ConservationThresholdNotRecognized, ConservationThresholdOutOfRange, debug, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ consistency_threshold_argument()

bool trimAlManager::consistency_threshold_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the consistency threshold argument.

inline

Definition at line 580 of file trimalManager.cpp.

References appearErrors, consistencyThreshold, ConsistencyThresholdNotRecognized, ConsistencyThresholdOutOfRange, debug, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ consistency_window_argument()

bool trimAlManager::consistency_window_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the Consistency Window argument.

inline

Definition at line 853 of file trimalManager.cpp.

References appearErrors, consistencyWindow, ConsistencyWindowValueNotRecognized, ConsistencyWindowValueOutOfRange, debug, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ create_or_use_similarity_matrix()

bool trimAlManager::create_or_use_similarity_matrix ( )

private

Method to create, load and use a similarity matrix, depending on alignment residue nature, if the user gave a specific similarity matrix, etc.

inline

Returns

Definition at line 1963 of file trimalManager.cpp.

References AA, alternative_matrix, statistics::similarityMatrix::alternativeSimilarityMatrices(), automated1, debug, statistics::similarityMatrix::defaultAASimMatrix(), statistics::similarityMatrix::defaultNTDegeneratedSimMatrix(), statistics::similarityMatrix::defaultNTSimMatrix(), DEG, DNA, Alignment::getAlignmentType(), ImpossibleToProcessMatrix, statistics::similarityMatrix::loadSimMatrix(), matrixFile, origAlig, reporting::reportManager::report(), RNA, statistics::Manager::setSimilarityMatrix(), statistics::similarityMatrix::similarityMatrix(), similarityThreshold, similMatrix, ssc, sst, Alignment::Statistics, strict, and strictplus.

Referenced by innerPerform().

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◆ delete_variables()

void trimAlManager::delete_variables ( )

Method to delete all variables that need to be deallocated.

inline

Definition at line 2242 of file trimalManager.cpp.

References backtransFile, backtranslationAlig, compareAlignmentsArray, CS, delColumns, delSequences, filesToCompare, forceFile, htmlOutFile, infile, matrixFile, origAlig, outfile, similMatrix, singleAlig, svgOutFile, svgStatsOutFile, tempAlig, and vcfs.

Referenced by ~trimAlManager().

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◆ examples()

void trimAlManager::examples ( )

private

Method to show the examples information about the program.

inline

Definition at line 2333 of file trimalManager.cpp.

References utils::TerminalColors::colors, and utils::ReplaceStringInPlace().

Referenced by help_arguments(), and parseArguments().

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◆ force_select_argument()

bool trimAlManager::force_select_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the force select argument.

inline

Definition at line 477 of file trimalManager.cpp.

References AlignmentNotLoaded, appearErrors, argumentLength, debug, Errored, forceFile, ForceSelectAndInArgumentsProvided, formatManager, infile, FormatHandling::FormatManager::loadAlignment(), NotRecognized, origAlig, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ gap_threshold_argument()

bool trimAlManager::gap_threshold_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the gap threshold argument.

inline

Definition at line 516 of file trimalManager.cpp.

References AbsoluteAndRelativeGapThreshold, AbsoluteGapThresholdLessThanZero, AbsoluteGapThresholdNotRecognized, appearErrors, debug, gapAbsoluteThreshold, gapThreshold, GapThresholdNotRecognized, GapThresholdOutOfRange, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ gap_window_argument()

bool trimAlManager::gap_window_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the Gap Window argument.

inline

Definition at line 818 of file trimalManager.cpp.

References appearErrors, debug, gapWindow, GapWindowValueNotRecognized, GapWindowValueOutOfRange, utils::isNumber(), NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ gappy_out_argument()

bool trimAlManager::gappy_out_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the gappyout argument.

inline

Definition at line 673 of file trimalManager.cpp.

References gappyout, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ getFormatManager()

FormatHandling::FormatManager & trimAlManager::getFormatManager ( )

Definition at line 2354 of file trimalManager.cpp.

References formatManager.

◆ help_arguments()

void trimAlManager::help_arguments	(	const int *	argc,
		char **	argv,
		int *	currentArg
	)

private

Method to parse information arguments as help and menu.

inline

Definition at line 279 of file trimalManager.cpp.

References examples(), Final, formatManager, FormatHandling::FormatManager::getInputFormatsAvailable(), FormatHandling::FormatManager::getOutputFormatsAvailable(), menu(), and NotRecognized.

Referenced by parseArguments().

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◆ html_out_argument()

bool trimAlManager::html_out_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the html output file.

inline

Definition at line 349 of file trimalManager.cpp.

References argumentLength, htmlOutFile, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ ignore_filter_argument()

trimAlManager::argumentReport trimAlManager::ignore_filter_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

inline

Definition at line 962 of file trimalManager.cpp.

References ignoreFilter, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ ignore_stop_codon_argument()

bool trimAlManager::ignore_stop_codon_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse ignore by stop codon argument.

inline

Definition at line 954 of file trimalManager.cpp.

References ignoreStopCodon, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ in_argument()

bool trimAlManager::in_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the input file argument.

inline

Definition at line 300 of file trimalManager.cpp.

References appearErrors, argumentLength, debug, Errored, forceFile, ForceSelectAndInArgumentsProvided, formatManager, infile, FormatHandling::FormatManager::loadAlignment(), NotRecognized, origAlig, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ innerPerform()

int trimAlManager::innerPerform ( )

private

inline

Definition at line 1803 of file trimalManager.cpp.

References appearErrors, blockSize, clean_alignment(), Alignment::Cleaning, columnNumbering, create_or_use_similarity_matrix(), keepSeqs, origAlig, output_reports(), postprocess_alignment(), print_statistics(), statistics::Manager::printCorrespondence(), save_alignment(), set_window_size(), Alignment::setBlockSize(), Alignment::setKeepSequencesFlag(), Cleaner::setTrimTerminalGapsFlag(), singleAlig, Alignment::Statistics, svg_stats_out(), svgStatsOutFile, and terminalOnly.

Referenced by perform().

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◆ keep_header_argument()

bool trimAlManager::keep_header_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the keepHeader argument.

inline

Definition at line 665 of file trimalManager.cpp.

References formatManager, FormatHandling::FormatManager::keepHeader, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ keep_seqs_argument()

bool trimAlManager::keep_seqs_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the keepSeqs argument.

inline

Definition at line 657 of file trimalManager.cpp.

References keepSeqs, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ matrix_argument()

bool trimAlManager::matrix_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the custom matrix argument.

inline

Definition at line 441 of file trimalManager.cpp.

References alternative_matrix, AlternativeMatrixNotRecognized, appearErrors, argumentLength, debug, matrixFile, NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ max_identity_argument()

bool trimAlManager::max_identity_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the max identity argument.

inline

Definition at line 756 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), maxIdentity, MaxIdentityNotRecognized, MaxIdentityOutOfRange, NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ menu()

void trimAlManager::menu ( )

private

Method to show the menu of the program.

inline

Definition at line 2305 of file trimalManager.cpp.

References utils::TerminalColors::colors, formatManager, FormatHandling::FormatManager::getInputFormatsAvailable(), FormatHandling::FormatManager::getOutputFormatsAvailable(), and utils::ReplaceStringInPlace().

Referenced by help_arguments(), and parseArguments().

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◆ min_coverage_argument()

trimAlManager::argumentReport trimAlManager::min_coverage_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

inline

Definition at line 987 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), minCoverage, MinCoverageLesserThan0, MinCoverageNotRecognized, NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ min_quality_argument()

trimAlManager::argumentReport trimAlManager::min_quality_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

inline

Definition at line 970 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), minQuality, MinQualityLesserThan0, MinQualityNotRecognized, NotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ no_all_gaps_argument()

bool trimAlManager::no_all_gaps_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the noallgaps argument.

inline

Definition at line 649 of file trimalManager.cpp.

References noallgaps, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ no_gaps_argument()

bool trimAlManager::no_gaps_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the nogaps argument.

inline

Definition at line 633 of file trimalManager.cpp.

References nogaps, NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ out_argument()

bool trimAlManager::out_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the output file pattern.

inline

Definition at line 339 of file trimalManager.cpp.

References argumentLength, NotRecognized, outfile, and Recognized.

Referenced by parseArguments().

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◆ out_format_arguments()

bool trimAlManager::out_format_arguments	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the output formats as -fasta -clustal or -formats [...].

inline

Definition at line 395 of file trimalManager.cpp.

References appearErrors, debug, Errored, formatManager, FormatHandling::FormatManager::getFormatFromToken(), NoFormatsSpecified, NotRecognized, oformats, OutputFormatNotRecognized, Recognized, and reporting::reportManager::report().

Referenced by parseArguments().

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◆ output_reports()

void trimAlManager::output_reports ( )

private

inline

Definition at line 1884 of file trimalManager.cpp.

References Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), appearErrors, debug, Alignment::filename, htmlOutFile, ImpossibleToGenerate, origAlig, utils::ReplaceString(), utils::ReplaceStringInPlace(), reporting::reportManager::report(), singleAlig, and svgOutFile.

Referenced by innerPerform().

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◆ parseArguments()

void trimAlManager::parseArguments	(	int	argc,
		char **	argv
	)

Method to parse arguments into usable structure in trimal.

Definition at line 74 of file trimalManager.cpp.

References appearErrors, automated1_argument(), back_trans_argument(), block_argument(), clusters_argument(), col_numbering_argument(), compareset, compareset_argument(), complementary_argument(), conservation_threshold_argument(), consistency_threshold_argument(), consistency_window_argument(), debug, Errored, examples(), Final, force_select_argument(), gap_threshold_argument(), gap_window_argument(), gappy_out_argument(), help_arguments(), html_out_argument(), ignore_filter_argument(), ignore_stop_codon_argument(), in_argument(), infile, keep_header_argument(), keep_seqs_argument(), matrix_argument(), max_identity_argument(), menu(), min_coverage_argument(), min_quality_argument(), no_all_gaps_argument(), no_gaps_argument(), NoInputFile, out_argument(), out_format_arguments(), ParameterNotFoundOrRepeated, performCompareset(), Recognized, remove_duplicates_argument(), reporting::reportManager::report(), residue_overlap_argument(), select_cols_argument(), seqs_select_argument(), sequence_overlap_argument(), similarity_threshold_argument(), similarity_window_argument(), split_by_stop_codon_argument(), stats_arguments(), strict_argument(), strict_plus_argument(), svg_out_argument(), svg_stats_argument(), terminal_only_argument(), timetracker_out_argument(), vcf_argument(), verbosity_argument(), and window_argument().

Referenced by main().

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◆ perform()

int trimAlManager::perform ( )

Method to perform the analysis if all checks have passed.

Returns: 0 if all went ok.
-1 if parsing arguments went wrong on previously steps
-2 if there was a problem with the similarity matrix.

Definition at line 1668 of file trimalManager.cpp.

References appearErrors, conservationThreshold, FormatHandling::BaseFormatHandler::extension, Alignment::filename, formatManager, FormatHandling::FormatManager::getFormatFromToken(), ignoreFilter, innerPerform(), minCoverage, minQuality, FormatHandling::BaseFormatHandler::name, oformats, origAlig, Alignment::originalNumberOfSequences, outfile, ngs::readVCF(), FormatHandling::FormatManager::replaceINtag(), utils::ReplaceString(), utils::ReplaceStringInPlace(), Alignment::seqsName, singleAlig, FormatHandling::FormatManager::splitAlignmentKeeping(), tempAlig, and vcfs.

Referenced by main().

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◆ performCompareset()

bool trimAlManager::performCompareset ( )

private

Method to check if multiple files comparison has been set correctly.
It also perform some calculations needed on comparfiles behaviour.

inline

Returns: False if dependencies check has passed
True otherwise

Definition at line 1864 of file trimalManager.cpp.

References appearErrors, compareset, ComparesetAndInArgumentsProvided, statistics::Consistency::Consistency(), CS, debug, forceFile, formatManager, infile, statistics::Consistency::perform(), and reporting::reportManager::report().

Referenced by parseArguments().

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◆ postprocess_alignment()

void trimAlManager::postprocess_alignment ( )

private

inline

Definition at line 2023 of file trimalManager.cpp.

References backtransFile, backtranslationAlig, Alignment::Cleaning, Cleaner::computeComplementaryAlig(), getComplementary, getComplementarySeq, Alignment::getTranslationCDS(), origAlig, Cleaner::removeOnlyTerminal(), singleAlig, tempAlig, and terminalOnly.

Referenced by innerPerform().

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◆ print_statistics()

void trimAlManager::print_statistics ( )

private

Method to print statistics requested.

inline

Definition at line 1915 of file trimalManager.cpp.

References compareset, statistics::Manager::consistency, statistics::Consistency::getValues(), origAlig, Alignment::printSeqIdentity(), Alignment::printSeqOverlap(), statistics::Manager::printStatisticsConservationColumns(), statistics::Manager::printStatisticsConservationTotal(), statistics::Consistency::printStatisticsFileAcl(), statistics::Consistency::printStatisticsFileColumns(), statistics::Manager::printStatisticsGapsColumns(), statistics::Manager::printStatisticsGapsTotal(), sfc, sft, sgc, sgt, sident, soverlap, ssc, sst, Alignment::Statistics, and stats.

Referenced by innerPerform().

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◆ processArguments()

bool trimAlManager::processArguments ( char * argv[] )

Method to process the information obtained by trimAlManager::parseArguments
It checks for argument incompatibilities and arguments dependencies.

Parameters

argv	Arguments passed to the program

Returns: True if all checks have passed
False otherwise

Definition at line 1004 of file trimalManager.cpp.

References appearErrors, automated1, automatedMethodCount, check_arguments_incompatibilities(), check_arguments_needs(), gappyout, noallgaps, nogaps, removeDuplicates, strict, and strictplus.

Referenced by main().

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◆ remove_duplicates_argument()

trimAlManager::argumentReport trimAlManager::remove_duplicates_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

inline

Definition at line 641 of file trimalManager.cpp.

References NotRecognized, Recognized, and removeDuplicates.

Referenced by parseArguments().

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◆ residue_overlap_argument()

bool trimAlManager::residue_overlap_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the residue overlap argument.

inline

Definition at line 705 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), NotRecognized, Recognized, reporting::reportManager::report(), ResidueOverlapNotRecognized, ResidueOverlapOutOfRange, and residuesOverlap.

Referenced by parseArguments().

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◆ save_alignment()

void trimAlManager::save_alignment ( )

private

inline

Definition at line 1840 of file trimalManager.cpp.

References appearErrors, debug, formatManager, oformats, outfile, reporting::reportManager::report(), FormatHandling::FormatManager::saveAlignment(), singleAlig, SomethingWentWrong_reportToDeveloper, and stats.

Referenced by innerPerform().

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◆ select_cols_argument()

bool trimAlManager::select_cols_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the select columns argument.

inline

Definition at line 615 of file trimalManager.cpp.

References appearErrors, debug, delColumns, NotRecognized, utils::readNumbers(), Recognized, reporting::reportManager::report(), selectCols, and SelectColsNotRecognized.

Referenced by parseArguments().

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◆ seqs_select_argument()

bool trimAlManager::seqs_select_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse que select sequences argument.

inline

Definition at line 739 of file trimalManager.cpp.

References appearErrors, debug, delSequences, NotRecognized, utils::readNumbers(), Recognized, reporting::reportManager::report(), selectSeqs, and SelectSeqsNotRecognized.

Referenced by parseArguments().

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◆ sequence_overlap_argument()

bool trimAlManager::sequence_overlap_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the sequence overlap argument.

inline

Definition at line 722 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), NotRecognized, Recognized, reporting::reportManager::report(), sequenceOverlap, SequencesOverlapNotRecognized, and SequencesOverlapOutOfRange.

Referenced by parseArguments().

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◆ set_window_size()

void trimAlManager::set_window_size ( )

private

Method to set correct window sizes depending on values for them given by the user.

inline

Definition at line 2226 of file trimalManager.cpp.

References gapWindow, origAlig, Alignment::setWindowsSize(), similarityWindow, and windowSize.

Referenced by innerPerform().

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◆ similarity_threshold_argument()

bool trimAlManager::similarity_threshold_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the similarity threshold argument.

inline

Definition at line 563 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), NotRecognized, Recognized, reporting::reportManager::report(), similarityThreshold, SimilarityThresholdNotRecognized, and SimilarityThresholdOutOfRange.

Referenced by parseArguments().

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◆ similarity_window_argument()

bool trimAlManager::similarity_window_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the Similarity Window argument.

inline

Definition at line 835 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), NotRecognized, Recognized, reporting::reportManager::report(), similarityWindow, SimilarityWindowValueNotRecognized, and SimilarityWindowValueOutOfRange.

Referenced by parseArguments().

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◆ split_by_stop_codon_argument()

bool trimAlManager::split_by_stop_codon_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse split by stop codon argument.

inline

Definition at line 946 of file trimalManager.cpp.

References NotRecognized, Recognized, and splitByStopCodon.

Referenced by parseArguments().

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◆ stats_arguments()

bool trimAlManager::stats_arguments	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse stats arguments.

inline

Definition at line 905 of file trimalManager.cpp.

References NotRecognized, sfc, sft, sgc, sgt, sident, soverlap, ssc, and sst.

Referenced by parseArguments().

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◆ strict_argument()

bool trimAlManager::strict_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the strict argument.

inline

Definition at line 681 of file trimalManager.cpp.

References NotRecognized, Recognized, and strict.

Referenced by parseArguments().

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◆ strict_plus_argument()

bool trimAlManager::strict_plus_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the strictplus argument.

inline

Definition at line 689 of file trimalManager.cpp.

References NotRecognized, Recognized, and strictplus.

Referenced by parseArguments().

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◆ svg_out_argument()

bool trimAlManager::svg_out_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the svg output file.

inline

Definition at line 367 of file trimalManager.cpp.

References argumentLength, NotRecognized, Recognized, and svgOutFile.

Referenced by parseArguments().

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◆ svg_stats_argument()

bool trimAlManager::svg_stats_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the svg stats output file.

inline

Definition at line 377 of file trimalManager.cpp.

References argumentLength, NotRecognized, Recognized, and svgStatsOutFile.

Referenced by parseArguments().

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◆ svg_stats_out()

void trimAlManager::svg_stats_out ( )

private

inline

Definition at line 1958 of file trimalManager.cpp.

References origAlig, Alignment::statSVG(), and svgStatsOutFile.

Referenced by innerPerform().

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◆ terminal_only_argument()

bool trimAlManager::terminal_only_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the terminal only argument.

inline

Definition at line 793 of file trimalManager.cpp.

References NotRecognized, Recognized, and terminalOnly.

Referenced by parseArguments().

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◆ timetracker_out_argument()

void trimAlManager::timetracker_out_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse InternalBenchmarker output argument.
Need to be checked before any other argument.

inline

Definition at line 359 of file trimalManager.cpp.

References NotRecognized, and Recognized.

Referenced by parseArguments().

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◆ vcf_argument()

void trimAlManager::vcf_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse vcf argument.

inline

Definition at line 322 of file trimalManager.cpp.

References NotRecognized, Recognized, and vcfs.

Referenced by parseArguments().

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◆ verbosity_argument()

bool trimAlManager::verbosity_argument	(	const int *	argc,
		char *	argv[]
	)

private

Method to parse the verbosity argument.
This check is done before any other check.
This is due to trimAl not performing any action if any help argument has been provided.
.

inline

Definition at line 251 of file trimalManager.cpp.

References debug, ERROR, INFO, reporting::reportManager::Level, NeedToSpecifyVerboseLevel, NONE, reporting::reportManager::report(), VerboseLevelNotRecognized, and WARNING.

Referenced by parseArguments().

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◆ window_argument()

bool trimAlManager::window_argument	(	const int *	argc,
		char *	argv[],
		int *	i
	)

private

Method to parse the Window argument.

inline

Definition at line 801 of file trimalManager.cpp.

References appearErrors, debug, utils::isNumber(), NotRecognized, Recognized, reporting::reportManager::report(), windowSize, WindowValueNotRecognized, and WindowValueOutOfRange.

Referenced by parseArguments().

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Friends And Related Function Documentation

◆ access_by

template<uint T>

friend struct access_by

friend

Definition at line 318 of file trimalManager.h.

◆ Catch::SectionInfo

friend struct Catch::SectionInfo

friend

Definition at line 66 of file trimalManager.h.

Member Data Documentation

◆ alternative_matrix

int trimAlManager::alternative_matrix = -1

Int that represents which alternative matrix to use, where '-1' means no alternative matrix, and '1' means degenerated_nt_identity.

Definition at line 121 of file trimalManager.h.

Referenced by check_similarity_matrix(), create_or_use_similarity_matrix(), and matrix_argument().

◆ appearErrors

bool trimAlManager::appearErrors = false

Flag to trace errors.

Definition at line 71 of file trimalManager.h.

◆ argumentLength

int trimAlManager::argumentLength = size_t(-1)

Temp variable to use when there is a need to copy an argument to a char array.

Definition at line 129 of file trimalManager.h.

Referenced by back_trans_argument(), force_select_argument(), html_out_argument(), in_argument(), matrix_argument(), out_argument(), svg_out_argument(), and svg_stats_argument().

◆ automated1

bool trimAlManager::automated1 = false

Flag to use the automated1 trimming method.

Definition at line 81 of file trimalManager.h.

Referenced by automated1_argument(), check_automated_methods_incompatibilities(), check_similarity_matrix(), check_thresholds_incompatibilities(), CleanResiduesAuto(), create_or_use_similarity_matrix(), and processArguments().

◆ automatedMethodCount

int trimAlManager::automatedMethodCount = -1

Integer counter of the automatic methods.
If the counter is bigger than 0, we are using an automatic method.
If the counter is bigger than 1, we are trying to use multiple automatic methods.

Definition at line 120 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_automated_methods_incompatibilities(), check_col_numbering(), check_file_aligned(), check_output_file_with_statistics(), check_output_relevance(), check_thresholds_incompatibilities(), clean_alignment(), and processArguments().

◆ backtransFile

char trimAlManager::backtransFile = nullptr

File to load the alignment containing the backtranslation information.

Definition at line 152 of file trimalManager.h.

Referenced by back_trans_argument(), check_and_prepare_coding_sequence(), check_backtranslation_infile_names_correspondence(), check_backtranslations(), check_coding_sequences_type(), check_input_file_with_coding_sequences_argument(), delete_variables(), and postprocess_alignment().

◆ backtranslationAlig

Alignment trimAlManager::backtranslationAlig = nullptr

Alignment used on the backtranslation functionality.

Definition at line 143 of file trimalManager.h.

Referenced by back_trans_argument(), check_and_prepare_coding_sequence(), check_backtranslation_infile_names_correspondence(), check_coding_sequences_type(), delete_variables(), and postprocess_alignment().

◆ blockSize

int trimAlManager::blockSize = -1

Block Size to use while trimming.

Definition at line 117 of file trimalManager.h.

Referenced by block_argument(), check_block_size(), check_select_cols_and_seqs_incompatibilities(), check_thresholds_incompatibilities(), and innerPerform().

◆ c

char trimAlManager::c

Temporal char variable.

Definition at line 147 of file trimalManager.h.

◆ clusters

int trimAlManager::clusters = -1

Number of most representative sequences we are going to use.

Definition at line 118 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_clusters_incompatibilities(), check_max_identity_incompatibilities(), check_output_relevance(), check_select_cols_and_seqs_incompatibilities(), CleanSequences(), and clusters_argument().

◆ columnNumbering

bool trimAlManager::columnNumbering = false

Flag to return column numbering in report.

Definition at line 75 of file trimalManager.h.

Referenced by check_col_numbering(), check_stats_incompatibilities(), col_numbering_argument(), and innerPerform().

◆ compare

ifstream trimAlManager::compare

Temporal variable to open files in trimAlManager::check_multiple_files_comparison function.

Note: This could be moved there

Definition at line 136 of file trimalManager.h.

Referenced by compareset_argument().

◆ compareAlignmentsArray

Alignment trimAlManager::compareAlignmentsArray = nullptr

Alignment Vector used on trimAlManager::check_multiple_files_comparison to compare them.

Note: This variable could be moved there.

Definition at line 144 of file trimalManager.h.

Referenced by delete_variables().

◆ compareset

int trimAlManager::compareset = nullptr

Pointer to the argument that contains the compareset file.

Definition at line 159 of file trimalManager.h.

Referenced by check_compareset_window_argument(), check_force_selection(), check_inFile_incompatibilities(), check_input_file_with_coding_sequences_argument(), check_similarity_matrix(), compareset_argument(), parseArguments(), performCompareset(), and print_statistics().

◆ conservationThreshold

float trimAlManager::conservationThreshold = -1

Similarity Threshold to use while trimming.

Definition at line 100 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_col_numbering(), check_combinations_among_thresholds_incompatibility(), check_output_file_with_statistics(), check_output_relevance(), check_thresholds_incompatibilities(), CleanResiduesNonAuto(), conservation_threshold_argument(), and perform().

◆ consistencyThreshold

float trimAlManager::consistencyThreshold = -1

Consistency Threshold to use while trimming.

Definition at line 103 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_col_numbering(), check_combinations_among_thresholds_incompatibility(), check_file_aligned(), check_inFile_incompatibilities(), check_output_relevance(), check_thresholds_incompatibilities(), CleanResiduesNonAuto(), and consistency_threshold_argument().

◆ consistencyWindow

int trimAlManager::consistencyWindow = -1

Consistency Window to use while trimming.

Definition at line 116 of file trimalManager.h.

Referenced by check_max_identity_incompatibilities(), check_similarity_matrix(), check_windows_incompatibilities(), consistency_window_argument(), and statistics::Consistency::perform().

◆ CS

statistics::Consistency* trimAlManager::CS = nullptr

Consistency Manager. We have to save the reference, while it is still not part of an alignment

Definition at line 172 of file trimalManager.h.

Referenced by delete_variables(), statistics::Consistency::perform(), and performCompareset().

◆ delColumns

int trimAlManager::delColumns = nullptr

Vector that contains the column indexes the user specified to be removed.

Definition at line 124 of file trimalManager.h.

Referenced by check_select_cols_and_seqs_incompatibilities(), CleanResiduesNonAuto(), delete_variables(), and select_cols_argument().

◆ delSequences

int trimAlManager::delSequences = nullptr

Vector that contains the sequence indexes the user specified to be removed.

Definition at line 125 of file trimalManager.h.

Referenced by check_select_cols_and_seqs_incompatibilities(), CleanSequences(), delete_variables(), and seqs_select_argument().

◆ filesToCompare

char trimAlManager::filesToCompare = nullptr

Vector containing the files to compare in trimAlManager::check_multiple_files_comparison function.

Note: This variable could be moved there.

Definition at line 164 of file trimalManager.h.

Referenced by delete_variables().

◆ forceFile

char trimAlManager::forceFile = nullptr

Forcefile to use in combination with multiple files comparison, to compare them against this.

Definition at line 148 of file trimalManager.h.

Referenced by check_force_selection(), check_inFile_incompatibilities(), check_input_file_with_coding_sequences_argument(), delete_variables(), force_select_argument(), in_argument(), and performCompareset().

◆ formatManager

FormatManager trimAlManager::formatManager

private

Read Write Machine that allows to manage formats easily.

Definition at line 306 of file trimalManager.h.

Referenced by back_trans_argument(), check_output_format(), force_select_argument(), getFormatManager(), help_arguments(), in_argument(), keep_header_argument(), menu(), out_format_arguments(), perform(), performCompareset(), and save_alignment().

◆ gapAbsoluteThreshold

int trimAlManager::gapAbsoluteThreshold = -1

Definition at line 122 of file trimalManager.h.

Referenced by check_absolute_gap_theshold(), and gap_threshold_argument().

◆ gappyout

bool trimAlManager::gappyout = false

Flag to use the gappyout trimming method.

Definition at line 78 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_thresholds_incompatibilities(), CleanResiduesAuto(), gappy_out_argument(), and processArguments().

◆ gapThreshold

float trimAlManager::gapThreshold = -1

Gap Threshold to use while trimming.

Definition at line 101 of file trimalManager.h.

Referenced by check_absolute_gap_theshold(), check_automated_manual_incompatibilities(), check_col_numbering(), check_combinations_among_thresholds_incompatibility(), check_file_aligned(), check_output_file_with_statistics(), check_output_relevance(), check_thresholds_incompatibilities(), CleanResiduesNonAuto(), and gap_threshold_argument().

◆ gapWindow

int trimAlManager::gapWindow = -1

Gap Window Size to use while trimming.

Definition at line 114 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_max_identity_incompatibilities(), check_similarity_matrix(), check_windows_incompatibilities(), gap_window_argument(), and set_window_size().

◆ getComplementary

bool trimAlManager::getComplementary = false

Flag to return the complementary alignment.

Definition at line 73 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), complementary_argument(), and postprocess_alignment().

◆ getComplementarySeq

bool trimAlManager::getComplementarySeq = false

Definition at line 74 of file trimalManager.h.

Referenced by complementary_argument(), and postprocess_alignment().

◆ htmlOutFile

char trimAlManager::htmlOutFile = nullptr

File to output the html report.

Definition at line 155 of file trimalManager.h.

Referenced by check_output_relevance(), check_outputs_coincidence(), delete_variables(), html_out_argument(), and output_reports().

◆ i

int trimAlManager::i = 1

Argument Iterator Variable.

Definition at line 111 of file trimalManager.h.

Referenced by check_inFile_incompatibilities().

◆ ignoreFilter

bool trimAlManager::ignoreFilter = false

Definition at line 96 of file trimalManager.h.

Referenced by check_vcf_incompatibility(), ignore_filter_argument(), and perform().

◆ ignoreStopCodon

bool trimAlManager::ignoreStopCodon = false

Flag to use the Ignore Stop Codon option.

Definition at line 95 of file trimalManager.h.

Referenced by check_and_prepare_coding_sequence(), check_backtranslations(), check_codon_behaviour_incompatibility(), and ignore_stop_codon_argument().

◆ infile

char trimAlManager::infile = nullptr

File to load the alignment when only one alignment has trimming interest.

Definition at line 150 of file trimalManager.h.

Referenced by check_file_aligned(), check_inFile_incompatibilities(), check_input_file_with_coding_sequences_argument(), check_output_format(), clean_alignment(), delete_variables(), force_select_argument(), in_argument(), parseArguments(), and performCompareset().

◆ keepSeqs

bool trimAlManager::keepSeqs = false

Flag to keep sequences in the alignment.

Definition at line 94 of file trimalManager.h.

Referenced by innerPerform(), and keep_seqs_argument().

◆ line

char trimAlManager::line

Temporal variable to read lines from a file.

Definition at line 164 of file trimalManager.h.

◆ matrixFile

char trimAlManager::matrixFile = nullptr

File that contains a user defined similarity matrix.

Definition at line 162 of file trimalManager.h.

Referenced by check_similarity_matrix(), create_or_use_similarity_matrix(), delete_variables(), and matrix_argument().

◆ maxIdentity

float trimAlManager::maxIdentity = -1

Max Identity to use while trimming.

Definition at line 106 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_max_identity_incompatibilities(), check_output_relevance(), check_select_cols_and_seqs_incompatibilities(), CleanSequences(), and max_identity_argument().

◆ minCoverage

float trimAlManager::minCoverage = -1

Definition at line 107 of file trimalManager.h.

Referenced by check_vcf_incompatibility(), min_coverage_argument(), and perform().

◆ minQuality

float trimAlManager::minQuality = -1

Definition at line 108 of file trimalManager.h.

Referenced by check_vcf_incompatibility(), min_quality_argument(), and perform().

◆ noallgaps

bool trimAlManager::noallgaps = false

Flag to use the noallgaps option.

Definition at line 77 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_thresholds_incompatibilities(), CleanResiduesAuto(), no_all_gaps_argument(), and processArguments().

◆ nogaps

bool trimAlManager::nogaps = false

Flag to use the nogaps option.

Definition at line 76 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_thresholds_incompatibilities(), CleanResiduesAuto(), no_gaps_argument(), and processArguments().

◆ oformats

std::vector< std::string > trimAlManager::oformats

Formats names we are going to output our trimmed alignment.

Definition at line 167 of file trimalManager.h.

Referenced by check_output_format(), out_format_arguments(), statistics::Consistency::perform(), perform(), and save_alignment().

◆ origAlig

Alignment trimAlManager::origAlig = nullptr

Main alignment used/loaded on trimAl in combination with singleAlig.

Definition at line 140 of file trimalManager.h.

Referenced by check_absolute_gap_theshold(), check_and_prepare_coding_sequence(), check_backtranslation_infile_names_correspondence(), check_backtranslations(), check_block_size(), check_clusters_incompatibilities(), check_file_aligned(), check_select_cols_and_seqs_incompatibilities(), clean_alignment(), CleanResiduesAuto(), CleanResiduesNonAuto(), CleanSequences(), create_or_use_similarity_matrix(), delete_variables(), force_select_argument(), in_argument(), innerPerform(), output_reports(), statistics::Consistency::perform(), perform(), postprocess_alignment(), print_statistics(), set_window_size(), and svg_stats_out().

◆ outfile

char trimAlManager::outfile = nullptr

File to output the trimmed alignment. This can contain tags which will be traduced to some variables:
[in] will be changed with the original filename.
[format] will be changed with the output format name specified.
[extension] will be changed to the correct format extension.

Definition at line 154 of file trimalManager.h.

Referenced by check_output_file_with_statistics(), check_outputs_coincidence(), delete_variables(), out_argument(), statistics::Consistency::perform(), perform(), and save_alignment().

◆ removeDuplicates

bool trimAlManager::removeDuplicates = false

Definition at line 97 of file trimalManager.h.

Referenced by CleanSequences(), processArguments(), and remove_duplicates_argument().

◆ residuesOverlap

float trimAlManager::residuesOverlap = -1

Residues Overlap to use while trimming.

Definition at line 104 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_file_aligned(), check_output_relevance(), check_residue_and_sequence_overlap(), CleanSequences(), and residue_overlap_argument().

◆ selectCols

bool trimAlManager::selectCols = false

Flag to select columns manually from the alignment.

Definition at line 91 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_col_numbering(), check_file_aligned(), check_output_relevance(), check_select_cols_and_seqs_incompatibilities(), and select_cols_argument().

◆ selectSeqs

bool trimAlManager::selectSeqs = false

Flag to select sequences manually from the alignment.

Definition at line 90 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_col_numbering(), check_file_aligned(), check_output_relevance(), check_select_cols_and_seqs_incompatibilities(), and seqs_select_argument().

◆ sequenceOverlap

float trimAlManager::sequenceOverlap = -1

Sequence Overlap to use while trimming.

Definition at line 105 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_file_aligned(), check_output_relevance(), check_residue_and_sequence_overlap(), CleanSequences(), and sequence_overlap_argument().

◆ sequencesLengths

int trimAlManager::sequencesLengths = nullptr

Vector that contains the sequences lengths of each sequence in the backtranslation option.

Note: This can be moved to trimAlManager::check_backtranslation_infile_names_correspondence() function or even deleted, as we don't really need to copy them in order to compare them with origAlig names.

Definition at line 126 of file trimalManager.h.

Referenced by check_backtranslation_infile_names_correspondence().

◆ sequencesNames

string trimAlManager::sequencesNames = nullptr

Temporal variable to use in backtranslation option to compare with infile.

Note: This variable may be deleted, as we don't need to copy the sequences names to compare them.

Definition at line 132 of file trimalManager.h.

Referenced by check_backtranslation_infile_names_correspondence().

◆ sfc

bool trimAlManager::sfc = false

Flag to show the Sum of Pairs scores per column.

Definition at line 86 of file trimalManager.h.

Referenced by check_inFile_incompatibilities(), print_statistics(), and stats_arguments().

◆ sft

bool trimAlManager::sft = false

Flag to show the Accumulated Sum of Pairs.

Definition at line 87 of file trimalManager.h.

Referenced by check_inFile_incompatibilities(), print_statistics(), and stats_arguments().

◆ sgc

bool trimAlManager::sgc = false

Flag to show the Gaps Scores per column.

Definition at line 82 of file trimalManager.h.

Referenced by print_statistics(), and stats_arguments().

◆ sgt

bool trimAlManager::sgt = false

Flag to show the Accumulated Gaps Scores.

Definition at line 83 of file trimalManager.h.

Referenced by print_statistics(), and stats_arguments().

◆ sident

bool trimAlManager::sident = false

Flag to show identity scores in the alignment.

Definition at line 88 of file trimalManager.h.

Referenced by print_statistics(), and stats_arguments().

◆ similarityThreshold

float trimAlManager::similarityThreshold = -1

Similarity Threshold to use while trimming.

Definition at line 102 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), check_col_numbering(), check_combinations_among_thresholds_incompatibility(), check_file_aligned(), check_output_file_with_statistics(), check_output_relevance(), check_similarity_matrix(), check_thresholds_incompatibilities(), CleanResiduesNonAuto(), create_or_use_similarity_matrix(), and similarity_threshold_argument().

◆ similarityWindow

int trimAlManager::similarityWindow = -1

Similarity Window to use while trimming.

Definition at line 115 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_max_identity_incompatibilities(), check_windows_incompatibilities(), set_window_size(), and similarity_window_argument().

◆ similMatrix

similarityMatrix trimAlManager::similMatrix = nullptr

Temporal Similarity Matrix.

Definition at line 137 of file trimalManager.h.

Referenced by create_or_use_similarity_matrix(), and delete_variables().

◆ singleAlig

Alignment trimAlManager::singleAlig = nullptr

Alignment obtained by making modifications to singleAlig or backtranslationAlig.

Definition at line 141 of file trimalManager.h.

Referenced by CleanResiduesAuto(), CleanResiduesNonAuto(), CleanSequences(), delete_variables(), innerPerform(), output_reports(), perform(), postprocess_alignment(), and save_alignment().

◆ soverlap

bool trimAlManager::soverlap = false

Flag to show overlap scores in the alignment.

Definition at line 89 of file trimalManager.h.

Referenced by print_statistics(), and stats_arguments().

◆ splitByStopCodon

bool trimAlManager::splitByStopCodon = false

Flag to use the SplitByCodonStop option.

Definition at line 92 of file trimalManager.h.

Referenced by check_and_prepare_coding_sequence(), check_backtranslations(), check_codon_behaviour_incompatibility(), and split_by_stop_codon_argument().

◆ ssc

bool trimAlManager::ssc = false

Flag to show the Similarity Scores per column.

Definition at line 84 of file trimalManager.h.

Referenced by check_similarity_matrix(), create_or_use_similarity_matrix(), print_statistics(), and stats_arguments().

◆ sst

bool trimAlManager::sst = false

Flag to show the Accumulated Similarity Scores.

Definition at line 85 of file trimalManager.h.

Referenced by check_similarity_matrix(), create_or_use_similarity_matrix(), print_statistics(), and stats_arguments().

◆ stats

int trimAlManager::stats = 0

Stats Flag to use in reporting. For each stat requested, this flag is decreased by one.

Definition at line 112 of file trimalManager.h.

Referenced by check_file_aligned(), check_output_file_with_statistics(), check_stats_incompatibilities(), statistics::Consistency::perform(), print_statistics(), and save_alignment().

◆ strict

bool trimAlManager::strict = false

Flag to use the strict trimming method.

Definition at line 79 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_similarity_matrix(), check_thresholds_incompatibilities(), CleanResiduesAuto(), create_or_use_similarity_matrix(), processArguments(), and strict_argument().

◆ strictplus

bool trimAlManager::strictplus = false

Flag to use the strictplus trimming method.

Definition at line 80 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_similarity_matrix(), check_thresholds_incompatibilities(), CleanResiduesAuto(), create_or_use_similarity_matrix(), processArguments(), and strict_plus_argument().

◆ svgOutFile

char trimAlManager::svgOutFile = nullptr

File to output the svg report.

Definition at line 156 of file trimalManager.h.

Referenced by check_output_relevance(), check_outputs_coincidence(), delete_variables(), output_reports(), and svg_out_argument().

◆ svgStatsOutFile

char trimAlManager::svgStatsOutFile = nullptr

File to output the svg graph showing the stats along the alignment.

Definition at line 157 of file trimalManager.h.

Referenced by check_output_relevance(), check_outputs_coincidence(), delete_variables(), innerPerform(), svg_stats_argument(), and svg_stats_out().

◆ tempAlig

Alignment trimAlManager::tempAlig = nullptr

Temporal alignment that allows us to make some changes to trimAlManager::singleAlig, destroy it and set trimAlManager::singleAlig to this.

Definition at line 142 of file trimalManager.h.

Referenced by CleanResiduesAuto(), CleanResiduesNonAuto(), CleanSequences(), delete_variables(), perform(), and postprocess_alignment().

◆ terminalOnly

bool trimAlManager::terminalOnly = false

Flag to use the Terminal Only option.

Definition at line 93 of file trimalManager.h.

Referenced by check_automated_manual_incompatibilities(), innerPerform(), postprocess_alignment(), and terminal_only_argument().

◆ vcfs

std::vector<std::string>* trimAlManager::vcfs = nullptr

Definition at line 68 of file trimalManager.h.

Referenced by check_file_aligned(), check_vcf_incompatibility(), delete_variables(), perform(), and vcf_argument().

◆ windowSize

int trimAlManager::windowSize = -1

Window Size to use while trimming.

Definition at line 113 of file trimalManager.h.

Referenced by check_automated_methods_incompatibilities(), check_compareset_window_argument(), check_max_identity_incompatibilities(), check_thresholds_dependencies(), check_windows_incompatibilities(), statistics::Consistency::perform(), set_window_size(), and window_argument().

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

/home/vfernandez/git/MyFork/include/trimalManager.h
/home/vfernandez/git/MyFork/source/trimalManager.cpp
/home/vfernandez/git/MyFork/Documentation/ClassDocumentation/trimAlManager/trimAlManager-parseArguments.dox
/home/vfernandez/git/MyFork/Documentation/ClassDocumentation/trimAlManager/trimAlManager-processArguments.dox
/home/vfernandez/git/MyFork/Documentation/ClassDocumentation/trimAlManager/trimAlManager-variables.dox
/home/vfernandez/git/MyFork/Documentation/ClassDocumentation/trimAlManager/trimalManager.dox

Classes

Public Types

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Friends

Argument Parsing methods

Process Arguments Methods

Detailed Description

Member Enumeration Documentation

◆ argumentReport

Constructor & Destructor Documentation

◆ trimAlManager()

◆ ~trimAlManager()

Member Function Documentation

◆ automated1_argument()

◆ back_trans_argument()

◆ block_argument()

◆ check_absolute_gap_theshold()

◆ check_and_prepare_coding_sequence()

◆ check_arguments_incompatibilities()

◆ check_arguments_needs()

◆ check_automated_manual_incompatibilities()

◆ check_automated_methods_incompatibilities()

◆ check_backtranslation_infile_names_correspondence()

◆ check_backtranslations()

◆ check_block_size()

◆ check_clusters_incompatibilities()

◆ check_coding_sequences_type()

◆ check_codon_behaviour_incompatibility()

◆ check_col_numbering()

◆ check_combinations_among_thresholds_incompatibility()

◆ check_compareset_window_argument()

◆ check_file_aligned()

◆ check_force_selection()

◆ check_inFile_incompatibilities()

◆ check_input_file_with_coding_sequences_argument()

◆ check_max_identity_incompatibilities()

◆ check_output_file_with_statistics()

◆ check_output_format()

◆ check_output_relevance()

◆ check_outputs_coincidence()

◆ check_residue_and_sequence_overlap()

◆ check_select_cols_and_seqs_incompatibilities()

◆ check_similarity_matrix()

◆ check_stats_incompatibilities()

◆ check_thresholds_dependencies()

◆ check_thresholds_incompatibilities()

◆ check_vcf_incompatibility()

◆ check_windows_incompatibilities()

◆ clean_alignment()

◆ CleanResiduesAuto()

◆ CleanResiduesNonAuto()

◆ CleanSequences()

◆ clusters_argument()

◆ col_numbering_argument()

◆ compareset_argument()

◆ complementary_argument()

◆ conservation_threshold_argument()

◆ consistency_threshold_argument()

◆ consistency_window_argument()

◆ create_or_use_similarity_matrix()

◆ delete_variables()

◆ examples()

◆ force_select_argument()

◆ gap_threshold_argument()

◆ gap_window_argument()

◆ gappy_out_argument()

◆ getFormatManager()

◆ help_arguments()

◆ html_out_argument()

◆ ignore_filter_argument()

◆ ignore_stop_codon_argument()

◆ in_argument()

◆ innerPerform()

◆ keep_header_argument()

◆ keep_seqs_argument()

◆ matrix_argument()

◆ max_identity_argument()