Utilitary methods dealing with sequence containers. More...

#include <Bpp/Seq/Container/SequenceContainerTools.h>

Public Member Functions
	SequenceContainerTools ()
virtual	~SequenceContainerTools ()
Static Public Member Functions
static SequenceContainer *	createContainerOfSpecifiedSize (const Alphabet *alphabet, size_t size)
	Create a container with void sequences.
static SequenceContainer *	createContainerWithSequenceNames (const Alphabet *alphabet, const std::vector< std::string > &seqNames) throw (Exception)
	Create a container with specified names.
template<class ContFrom , class ContTo , class Seq >
static void	convertContainer (const ContFrom &input, ContTo &output)
	Generic function which creates a new container from another one, by specifying the class of sequence to be stored.
static void	getSelectedSequences (const OrderedSequenceContainer &sequences, const SequenceSelection &selection, SequenceContainer &outputCont) throw (Exception)
	Add a specified set of sequences from a container to another.
static void	getSelectedSequences (const SequenceContainer &sequences, const std::vector< std::string > &selection, SequenceContainer &outputCont, bool strict=true) throw (Exception)
	Add a specified set of sequences from a container to another.
static void	keepOnlySelectedSequences (OrderedSequenceContainer &sequences, const SequenceSelection &selection)
	Remove all sequences that are not in a given selection from a given container.
static bool	sequencesHaveTheSameLength (const SequenceContainer &sequences)
	Check if all sequences in a SequenceContainer have the same length.
static void	getCounts (const SequenceContainer &sequences, std::map< int, int > &)
	Compute base counts.
static void	getFrequencies (const SequenceContainer &sequences, std::map< int, double > &f, double pseudoCount=0)
	Compute base frequencies.
static void	append (SequenceContainer &seqCont1, const SequenceContainer &seqCont2, bool checkNames=true) throw (Exception)
	Append all the sequences of a SequenceContainer to the end of another.
static void	append (SequenceContainer &seqCont1, const OrderedSequenceContainer &seqCont2, bool checkNames=true) throw (Exception)
	Append all the sequences of a SequenceContainer to the end of another, OrderedSequenceContainer implementation.
static void	merge (const SequenceContainer &seqCont1, const SequenceContainer &seqCont2, SequenceContainer &outputCont) throw (Exception)
	Concatenate the sequences from two containers.
static void	convertAlphabet (const SequenceContainer &seqCont, SequenceContainer &outputCont) throw (Exception)
	Convert a SequenceContainer with a new alphabet.
static SequenceContainer *	getCodonPosition (const SequenceContainer &sequences, size_t pos) throw (AlphabetException)
	Extract a certain position (1, 2 or 3) from a container of codon sequences and returns the resulting nucleotide container.

Detailed Description

Utilitary methods dealing with sequence containers.

Definition at line 61 of file SequenceContainerTools.h.

Constructor & Destructor Documentation

bpp::SequenceContainerTools::SequenceContainerTools ( ) [inline]

Definition at line 65 of file SequenceContainerTools.h.

virtual bpp::SequenceContainerTools::~SequenceContainerTools ( ) [inline, virtual]

Definition at line 66 of file SequenceContainerTools.h.

Member Function Documentation

static void bpp::SequenceContainerTools::append	(	SequenceContainer &	seqCont1,
		const SequenceContainer &	seqCont2,
		bool	checkNames = `true`
	)		throw (Exception) `[inline, static]`

Append all the sequences of a SequenceContainer to the end of another.

Parameters:

seqCont1	The SequenceContainer in which the sequences will be added.
seqCont2	The SequenceContainer from which the sequences are taken.
checkNames	Tell if the sequence names should be check for unicity.

Definition at line 214 of file SequenceContainerTools.h.

static void bpp::SequenceContainerTools::append	(	SequenceContainer &	seqCont1,
		const OrderedSequenceContainer &	seqCont2,
		bool	checkNames = `true`
	)		throw (Exception) `[inline, static]`

Append all the sequences of a SequenceContainer to the end of another, OrderedSequenceContainer implementation.

Parameters:

seqCont1	The SequenceContainer in which the sequences will be added.
seqCont2	The SequenceContainer from which the sequences are taken.
checkNames	Tell if the sequence names should be check for unicity.

Definition at line 228 of file SequenceContainerTools.h.

References bpp::SequenceContainer::addSequence(), bpp::OrderedSequenceContainer::getNumberOfSequences(), and bpp::OrderedSequenceContainer::getSequence().

static void bpp::SequenceContainerTools::convertAlphabet	(	const SequenceContainer &	seqCont,
		SequenceContainer &	outputCont
	)		throw (Exception) `[inline, static]`

Convert a SequenceContainer with a new alphabet.

This method assume that the original container has proper sequence names. Names will be checked only if the output container is not empty.

Parameters:

seqCont	The container to convert.
outputCont	A container (most likely empty) with an alphabet into which the container will be converted.

Definition at line 272 of file SequenceContainerTools.h.

template<class ContFrom , class ContTo , class Seq >

static void bpp::SequenceContainerTools::convertContainer	(	const ContFrom &	input,
		ContTo &	output
	)		`[inline, static]`

Generic function which creates a new container from another one, by specifying the class of sequence to be stored.

Compared to several copy constructors, this function allows to change the class of the inner sequence class used for storing sequences. The function used the addSequence method, so that it can also be used to concatenate containers.

Parameters:

input	The container to copy.
output	The container where new sequences will be appended.

Definition at line 112 of file SequenceContainerTools.h.

SequenceContainer * SequenceContainerTools::createContainerOfSpecifiedSize	(	const Alphabet *	alphabet,
		size_t	size
	)		`[static]`

Create a container with $n$ void sequences.

A new VectorSequenceContainer with the specified alphabet is created. The destruction of this new container is up to the user. Sequences have name "0", "1",... "n-1" and no content and comments.

Parameters:

alphabet	The alphabet to use in the container.
size	The number of sequences in the container.

Returns:: A pointer toward a newly created container.

Definition at line 53 of file SequenceContainerTools.cpp.

References bpp::VectorSequenceContainer::addSequence().

SequenceContainer * SequenceContainerTools::createContainerWithSequenceNames	(	const Alphabet *	alphabet,
		const std::vector< std::string > &	seqNames
	)		throw (Exception) `[static]`

Create a container with specified names.

A new VectorSequenceContainer with the specified alphabet is created. The destruction of this new container is up to the user. Sequences have the specified names and no content and comments.

Parameters:

alphabet	The alphabet to use in the container.
seqNames	The names of the sequences.

Returns:: A pointer toward a newly created container.

Exceptions:

Exception If two sequence names are not unique.

Definition at line 65 of file SequenceContainerTools.cpp.

References bpp::SequenceContainer::setSequencesNames().

SequenceContainer * SequenceContainerTools::getCodonPosition	(	const SequenceContainer &	sequences,
		size_t	pos
	)		throw (AlphabetException) `[static]`

Extract a certain position (1, 2 or 3) from a container of codon sequences and returns the resulting nucleotide container.

Parameters:

sequences	The input sequence container, with codon alphabet.
pos	The codon position to retrieve.

Returns:: A SequenceContainer with a nucleotide alphabet.

Exceptions:

AlphabetException If input sequences are not registered with a codon alphabet.

Definition at line 201 of file SequenceContainerTools.cpp.

References bpp::VectorSequenceContainer::addSequence(), bpp::AbstractSequenceContainer::getContent(), bpp::WordAlphabet::getNPosition(), and bpp::CodonAlphabet::getNucleicAlphabet().

void SequenceContainerTools::getCounts	(	const SequenceContainer &	sequences,
		std::map< int, int > &	f
	)		`[static]`

Compute base counts.

Example of usage: getting the GC count from a sequence container. map<int, int> counts; SequenceContainerTools::getCounts(myContainer, counts); //My container is previously defined. int GCcontent = counts[1] + counts[2] ;

States are stored as their int code.

Definition at line 184 of file SequenceContainerTools.cpp.

References bpp::SequenceContainer::getContent(), and bpp::SequenceContainer::getSequencesNames().

void SequenceContainerTools::getFrequencies	(	const SequenceContainer &	sequences,
		std::map< int, double > &	f,
		double	pseudoCount = `0`
	)		`[static]`

Compute base frequencies.

Example of usage: getting the GC content from a sequence container. map<int, double> freqs; SequenceContainerTools::getFrequencies(myContainer, freqs); //My container is previously defined. double GCcontent = (freqs[1] + freqs[2]) / (freqs[0] + freqs[1] + freqs[2] + freqs[3]);

States are stored as their int code.

Definition at line 151 of file SequenceContainerTools.cpp.

References bpp::SequenceContainer::getAlphabet(), bpp::SequenceContainer::getContent(), bpp::SequenceContainer::getSequencesNames(), and bpp::Alphabet::getSize().

void SequenceContainerTools::getSelectedSequences	(	const OrderedSequenceContainer &	sequences,
		const SequenceSelection &	selection,
		SequenceContainer &	outputCont
	)		throw (Exception) `[static]`

Add a specified set of sequences from a container to another.

Sequences are specified by their position, beginning at 0. Name verification will be performed, only if the output container is not empty, based on the assumption that the container passed as argument is a correct one. Redundant selection is not checked, so be careful with what you're doing!

Author:: Julien Dutheil

Parameters:

sequences	The container from wich sequences are to be taken.
selection	The positions of all sequences to retrieve.
outputCont	A container where the selection should be added.

Exceptions:

Exception In case of bad sequence name, alphabet mismatch, etc.

Definition at line 77 of file SequenceContainerTools.cpp.

Referenced by bpp::SiteContainerTools::merge().

void SequenceContainerTools::getSelectedSequences	(	const SequenceContainer &	sequences,
		const std::vector< std::string > &	selection,
		SequenceContainer &	outputCont,
		bool	strict = `true`
	)		throw (Exception) `[static]`

Add a specified set of sequences from a container to another.

Sequences are specified by their names. Name verification will be performed, only if the output container is not empty, based on the assumption that the container passed as argument is a correct one. Redundant selection is not checked, so be careful with what you're doing!

Author:: Julien Dutheil

Parameters:

sequences	The container from wich sequences are to be taken.
selection	The names of all sequences to retrieve.
outputCont	A container where the selection should be added.
strict	If yes, trying to select a sequence that is not present will raise an exception. If no, only available sequence will be added.

Exceptions:

Exception In case of bad sequence name, alphabet mismatch, etc.

Definition at line 91 of file SequenceContainerTools.cpp.

void SequenceContainerTools::keepOnlySelectedSequences	(	OrderedSequenceContainer &	sequences,
		const SequenceSelection &	selection
	)		`[static]`

Remove all sequences that are not in a given selection from a given container.

A new VectorSequenceContainer is created with specified sequences. The destruction of the container is up to the user. Sequences are specified by their position, beginning at 0. Redundant selection is not checked, so be careful with what you're doing!

Parameters:

sequences	The container from wich sequences are to be taken.
selection	The positions of all sequences to retrieve.

Returns:: A new container with all selected sequences.

Definition at line 113 of file SequenceContainerTools.cpp.

References bpp::OrderedSequenceContainer::deleteSequence(), and bpp::OrderedSequenceContainer::getSequencesNames().

static void bpp::SequenceContainerTools::merge	(	const SequenceContainer &	seqCont1,
		const SequenceContainer &	seqCont2,
		SequenceContainer &	outputCont
	)		throw (Exception) `[inline, static]`

Concatenate the sequences from two containers.

This method will not check the original sequence names for unicity. If sequences do not have a unique name, then the resulting merged container will contain the first sequence with the given duplicated name.

Author:: Julien Dutheil

Parameters:

seqCont1	First container.
seqCont2	Second container. This container must contain sequences with the same names as in seqcont1. Additional sequences will be ignored.
outputCont	Output sequence container to which concatenated sequences will be added.

Exceptions:

AlphabetMismatchException If the alphabet in the 3 containers do not match.

Definition at line 249 of file SequenceContainerTools.h.

References bpp::BasicSequence::append().

bool SequenceContainerTools::sequencesHaveTheSameLength ( const SequenceContainer & sequences ) [static]

Check if all sequences in a SequenceContainer have the same length.

Parameters:

sequences The container to check.

Returns:: True is all sequence have the same length.

Definition at line 135 of file SequenceContainerTools.cpp.

References bpp::SequenceContainer::getSequence(), bpp::SequenceContainer::getSequencesNames(), and bpp::SymbolList::size().

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

Bpp/Seq/Container/SequenceContainerTools.h
Bpp/Seq/Container/SequenceContainerTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation