This class provides some common tools for applications. More...

#include <Bpp/Seq/App/SequenceApplicationTools.h>

Public Member Functions
	SequenceApplicationTools ()

virtual	~SequenceApplicationTools ()

Static Public Member Functions
static Alphabet *	getAlphabet (std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool allowGeneric=false, int warn=1) throw (Exception)
	Build an Alphabet object according to options. More...

static GeneticCode *	getGeneticCode (const NucleicAlphabet *alphabet, const std::string &description) throw (Exception)
	Build a GeneticCode object according to options. More...

static AlphabetIndex1 *	getAlphabetIndex1 (const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true) throw (Exception)
	Build a AlphabetIndex1 object for a given alphabet. More...

static AlphabetIndex2 *	getAlphabetIndex2 (const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true) throw (Exception)
	Build a AlphabetIndex2 object for a given alphabet. More...

static SequenceContainer *	getSequenceContainer (const Alphabet *alpha, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a SequenceContainer object according to options. More...

static VectorSiteContainer *	getSiteContainer (const Alphabet *alpha, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)
	Build a SiteContainer object according to options. More...

static VectorSiteContainer *	getSitesToAnalyse (const SiteContainer &allSites, std::map< std::string, std::string > &params, std::string suffix="", bool suffixIsOptional=true, bool gapAsUnknown=true, bool verbose=true, int warn=1)
	Retrieves sites suitable for the analysis. More...

static void	writeSequenceFile (const SequenceContainer &sequences, std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)
	Write a sequence file according to options. More...

static void	writeAlignmentFile (const SiteContainer &sequences, std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)
	Write a sequence alignment file according to options. More...

Detailed Description

This class provides some common tools for applications.

The functions parse some option file, create corresponding objects and send a pointer toward it.

The option files are supposed to follow this simple format:

parameterName = parameterContent

with one parameter per line.

See also: ApplicationTools

Definition at line 70 of file SequenceApplicationTools.h.

Constructor & Destructor Documentation

◆ SequenceApplicationTools()

bpp::SequenceApplicationTools::SequenceApplicationTools ( )

inline

Definition at line 73 of file SequenceApplicationTools.h.

◆ ~SequenceApplicationTools()

virtual bpp::SequenceApplicationTools::~SequenceApplicationTools ( )

inlinevirtual

Definition at line 74 of file SequenceApplicationTools.h.

Member Function Documentation

◆ getAlphabet()

Alphabet * SequenceApplicationTools::getAlphabet	(	std::map< std::string, std::string > &	params,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	verbose = `true`,
		bool	allowGeneric = `false`,
		int	warn = `1`
	)
throw	(	Exception
	)

static

Build an Alphabet object according to options.

Options used are:

alphabet = [DNA|RNA|Protein], the alphabet type to use. = [DNA|RNA|Protein](length=n) a word-alphabet of words with length n = [EchinodermMitochondrialCodonAlphabet | InvertebrateMitochondrialCodonAlphabet | InvertebrateMitochondrialCodonAlphabet | StandardCodonAlphabet | VertebrateMitochondrialCodonAlphabet]([alphn=NA|RNA]) a codon-alphabet

Parameters

params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
allowGeneric	Tell if generic alphabets can be used.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns: A new Alphabet object according to options specified.

Definition at line 73 of file SequenceApplicationTools.cpp.

References bpp::AlphabetTools::isNucleicAlphabet().

◆ getAlphabetIndex1()

AlphabetIndex1 * SequenceApplicationTools::getAlphabetIndex1	(	const Alphabet *	alphabet,
		const std::string &	description,
		const std::string &	message = `"Alphabet distance:"`,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Build a AlphabetIndex1 object for a given alphabet.

Parameters

alphabet	The alphabet to use. This is currently only used for assessing the type of distance allowed.
description	Which distance to use. See the Bio++ Program Suite reference manual for a description of the syntax.
message	To be displayed when parsing.
verbose	Tell if some info should be displayed while parsing.

Returns: A new AlphabetIndex1 object.

Exceptions

Exception in case of bad description.

Definition at line 213 of file SequenceApplicationTools.cpp.

References bpp::BppOAlphabetIndex1Format::read().

◆ getAlphabetIndex2()

AlphabetIndex2 * SequenceApplicationTools::getAlphabetIndex2	(	const Alphabet *	alphabet,
		const std::string &	description,
		const std::string &	message = `"Alphabet distance:"`,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Build a AlphabetIndex2 object for a given alphabet.

Parameters

alphabet	The alphabet to use. This is currently only used for assessing the type of distance allowed.
description	Which distance to use. See the Bio++ Program Suite reference manual for a description of the syntax.
message	To be displayed when parsing.

Returns: A new AlphabetIndex2 object.

Parameters

verbose Tell if some info should be displayed while parsing.

Exceptions

Exception in case of bad description.

Definition at line 220 of file SequenceApplicationTools.cpp.

References bpp::BppOAlphabetIndex2Format::read().

◆ getGeneticCode()

GeneticCode * SequenceApplicationTools::getGeneticCode	(	const NucleicAlphabet *	alphabet,
		const std::string &	description
	)
throw	(	Exception
	)

static

Build a GeneticCode object according to options.

Parameters

alphabet	pointer to the NucleicAlphabet
description	for the name of the GeneticCode: [EchinodermMitochondrialGeneticCode \| InvertebrateMitochondrialGeneticCode \| InvertebrateMitochondrialGeneticCode \| StandardGeneticCode \| VertebrateMitochondrialGeneticCode]

Returns: A new GeneticCode object

Exceptions

Exception in case of bad description.

Definition at line 187 of file SequenceApplicationTools.cpp.

◆ getSequenceContainer()

SequenceContainer * SequenceApplicationTools::getSequenceContainer	(	const Alphabet *	alpha,
		std::map< std::string, std::string > &	params,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	verbose = `true`,
		int	warn = `1`
	)

static

Build a SequenceContainer object according to options.

The sequences do not have to be aligned. The supported sequence formats are Fasta, DCSE, Clustal, Mase, Phylip and GenBank.

See the Bio++ program suite manual for a full description of the syntax.

Parameters

alpha	The alphabet to use in the container.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns: A new VectorSequenceContainer object according to options specified.

See also: getSiteContainer to read an alignment.

Definition at line 228 of file SequenceApplicationTools.cpp.

References bpp::BppOSequenceReaderFormat::read().

◆ getSiteContainer()

VectorSiteContainer * SequenceApplicationTools::getSiteContainer	(	const Alphabet *	alpha,
		std::map< std::string, std::string > &	params,
		const std::string &	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	verbose = `true`,
		int	warn = `1`
	)

static

Build a SiteContainer object according to options.

Sequences in file must be aligned. The supported sequence formats are Fasta, DCSE, Clustal, Mase and Phylip.

See the Bio++ program suite manual for a full description of the syntax.

Parameters

alpha	The alphabet to use in the container.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns: A new VectorSiteContainer object according to options specified.

Definition at line 252 of file SequenceApplicationTools.cpp.

References bpp::VectorSiteContainer::addSequence(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::VectorSiteContainer::getSequence(), bpp::BppOAlignmentReaderFormat::getUnparsedArguments(), bpp::AlphabetTools::isRNYAlphabet(), bpp::BppOAlignmentReaderFormat::read(), bpp::VectorSiteContainer::reindexSites(), and bpp::SequenceTools::RNYslice().

◆ getSitesToAnalyse()

VectorSiteContainer * SequenceApplicationTools::getSitesToAnalyse	(	const SiteContainer &	allSites,
		std::map< std::string, std::string > &	params,
		std::string	suffix = `""`,
		bool	suffixIsOptional = `true`,
		bool	gapAsUnknown = `true`,
		bool	verbose = `true`,
		int	warn = `1`
	)

static

Retrieves sites suitable for the analysis.

Options used are:

sequence.sites_to_use = [all|complete|nogap].

If the 'complete' option is used, only fully resolve site will be taken into account. If the 'nogap' option is used, only sites without gap will be taken into account. If 'gapAsUnknown' is set to true and the all option is selected, gaps will be changed to 'unknown' character is sequences.

sequence.max_gap_allowed = [57%|30] If a % sign fallow the number, it is taken to be a frequence (in percent). This specify the maximum amount of gaps allowed for each site. Sites not satisfying this amount will be removed. A value of 100% will remove all gap-only sites, a value >100% will keep all sites.

Parameters

allSites	The site container from which sites must be retrieved.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
suffixIsOptional	Tell if the suffix is absolutely required.
gapAsUnknown	Convert gaps to unknown characters.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Returns: A new VectorSiteContainer object containing sites of interest.

Definition at line 386 of file SequenceApplicationTools.cpp.

References bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainer::deleteSite(), bpp::SequenceContainer::getAlphabet(), bpp::SiteContainerTools::getCompleteSites(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getFrequencies(), bpp::CodonAlphabet::getNucleicAlphabet(), bpp::OrderedSequenceContainer::getNumberOfSequences(), bpp::SiteContainer::getNumberOfSites(), bpp::SiteContainer::getSite(), bpp::SiteContainerTools::getSitesWithoutGaps(), bpp::Alphabet::getSize(), and bpp::SiteContainerTools::removeStopCodonSites().

◆ writeAlignmentFile()

void SequenceApplicationTools::writeAlignmentFile	(	const SiteContainer &	sequences,
		std::map< std::string, std::string > &	params,
		const std::string &	suffix = `""`,
		bool	verbose = `true`,
		int	warn = `1`
	)

static

Write a sequence alignment file according to options.

The supported sequence formats are Fasta, Mase and Phylip.

See the Bio++ program suite manual for a full description of the syntax.

Parameters

sequences	The aligned sequences to write.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 577 of file SequenceApplicationTools.cpp.

References bpp::BppOAlignmentWriterFormat::read().

◆ writeSequenceFile()

void SequenceApplicationTools::writeSequenceFile	(	const SequenceContainer &	sequences,
		std::map< std::string, std::string > &	params,
		const std::string &	suffix = `""`,
		bool	verbose = `true`,
		int	warn = `1`
	)

static

Write a sequence file according to options.

The supported sequence formats are Fasta and Mase.

See the Bio++ program suite manual for a full description of the syntax.

See also: writeSequenceFile(SiteContainer) for writing alignments, with more output formats.

Parameters

sequences	The sequences to write.
params	The attribute map where options may be found.
suffix	A suffix to be applied to each attribute name.
verbose	Print some info to the 'message' output stream.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).