Handles a sequence alignment. More...

#include <Align.hpp>

Inheritance diagram for Align:

Public Member Functions
	Align ()
	Creates an empty alignment. More...

	Align (unsigned int number_of_sequences, unsigned int alignment_length, char const const const cstring_array)
	Creates an alignment from a data matrix. More...

	Align (unsigned int number_of_sequences, unsigned int alignment_length)
	Creates an alignment with given dimensions. More...

	Align (const Align &align)
	Copy constructor. More...

	Align (const Container &container)
	Copy constructor accepting a Container object. More...

Align &	operator= (const Align &align)
	Copy operator. More...

Align &	operator= (const Container &container)
	Copy operator accepting a Container object. More...

virtual	~Align ()
	Destructor. More...

virtual unsigned int	append (const char name, const char sequence, unsigned int group=0)
	Adds a sequence. More...

virtual unsigned int	removePosition (unsigned int pos)
	Removes a position (column) of the alignment. More...

virtual unsigned int	remove (unsigned int pos)
	Removes a sequence from the alignment. More...

virtual void	sequence (unsigned int seq, const char *sequence)
	Replace a sequence string. More...

virtual const char *	sequence (unsigned int pos) const
	Gets the name of a given sequence. More...

virtual unsigned int	ls () const
	Alignment length. More...

virtual unsigned int	ls (unsigned int pos) const
	Length of a given sequence. More...

char	character (unsigned int s, unsigned int p) const
	Fast and unsecure accessor. More...

virtual char	get (unsigned int sequence, unsigned int position) const
	Gets a nucleotide. More...

virtual void	set (unsigned int sequence, unsigned position, char ch)
	Sets a matrix position to a new character. More...

void	binSwitch (unsigned int pos)
	Reverse a given column in binary data. More...

Align	vslice (std::vector< unsigned int > list_of_sites)
	Extracts specified positions (columns) of the alignment. More...

Align	vslice (unsigned int a, unsigned int b)
	Extracts a range of positions (columns) More...

virtual void	clear ()
	Deletes all the content of the object. More...

unsigned int	numberOfSequences () const
	Same as ns() More...

unsigned int	numberOfSites () const
	Same as ls() More...

unsigned int	populationLabel (unsigned int sequenceIndex) const
	Gets a group label (insecure) More...

double	sitePosition (unsigned int position) const
	Just return the passed value. More...

Public Member Functions inherited from Container
	Container ()
	Creates an empty object. More...

	Container (const Container &source)
	Copy constructor. More...

Container &	operator= (const Container &source)
	Assignment operator. More...

	Container (unsigned int number_of_sequences, char const const const cstring_array)
	Creates an object from a data matrix. More...

virtual	~Container ()
	Destructor. More...

virtual void	name (unsigned int pos, const char *name)
	Changes the name of a given sequence. More...

virtual void	group (unsigned int pos, unsigned int group)
	Changes the group index of a given sequence. More...

Container	hslice (unsigned int a, unsigned int b) const
	Extracts a range of sequences. More...

unsigned int	ns () const
	Gets the number of sequences. More...

virtual const char *	name (unsigned int pos) const
	Gets the name of the a given sequence. More...

virtual unsigned int	group (unsigned int pos) const
	Gets the group index of a given sequence. More...

bool	isEqual () const
	Checks if all lengths are equal. More...

unsigned int	equalize (char ch='?')
	Equalizes sequence lengths. More...

int	find (const char *string, bool strict=true) const
	Finds a sequence by its name. More...

Protected Member Functions
virtual void	appendSequence (unsigned int pos, const char *sequence)
	This function is not available for alignments.

virtual void	init ()

virtual void	setFromSource (unsigned int number_of_sequences, unsigned int alignment_length, const char const const cstring_array)

virtual void	copyObject (const Container &)

virtual void	copyObject (const Align &)

Protected Member Functions inherited from Container
virtual void	setFromSource (unsigned int number_of_sequences, const char const const cstring_array)

virtual void	getNamesAndGroups (const Container &)

Protected Attributes
unsigned int	_ls

Protected Attributes inherited from Container
unsigned int	_ns

unsigned int *	lnames

char **	names

char **	sequences

unsigned int *	groups

Detailed Description

Handles a sequence alignment.

Creation from a file or string stream should be performed using the class Fasta. Align objects can be created by deep copy from both Align and Container type. In the latter case, the length are artificially equalized by "?" characters. Align objects can be created from a DataMatrix object (and all the way arround) using the specific class DMAConverter.

Sequences are represented by two strings (name and sequence) and an integer (group) that can be accessed or modified by index.The order of sequences is guaranteed to be conserved, as if Align was a list of triplets (name, sequence, group).

The data matrix is implemented as continuous array (char**) and allows efficient access and modification of data. For very large data matrices you might claim immediately the required memory using the constructor Align(unsigned int, char**).

Constructor & Destructor Documentation

Align ( )

Creates an empty alignment.

Align	(	unsigned int	number_of_sequences,
		unsigned int	alignment_length,
		char const const const	cstring_array
	)

Creates an alignment from a data matrix.

Allows you to create an object from data stored in a char* array. The array's dimensions must be passed to the constructor, and as a result there is not need to terminate each sequence by a NULL character.

Parameters

number_of_sequences	the number of sequences (the length of the first dimension of the array).
alignment_length	the length of sequences (the length of all lines of the array).
cstring_array	the pointer to the data matrix.

Align	(	unsigned int	number_of_sequences,
		unsigned int	alignment_length
	)

Creates an alignment with given dimensions.

Allows you to allocate directly a data matrix of a given size. Names are empty strings, groups 0, and all characters are ?.

Parameters

number_of_sequences	the number of sequences (the length of the first dimension of the array).
alignment_length	the length of sequences (the length of all lines of the array).

Align ( const Align & align )

Copy constructor.

Align ( const Container & container )

Copy constructor accepting a Container object.

All but the longest sequences are padded with ? to match the longest sequence's length.

~Align ( )

virtual

Destructor.

Member Function Documentation

unsigned int append	(	const char *	name,
		const char *	sequence,
		unsigned int	group = `0`
	)

virtual

Adds a sequence.

If the object already contains at least one sequence, the new sequence must have the same length. Otherwise, a EggUnalignedError is raised.

Parameters

name	the name of the sequence.
sequence	the sequence string.
group	the group index of the sequence.

Returns: The new number of sequences.

Reimplemented from Container.

void binSwitch ( unsigned int pos )

Reverse a given column in binary data.

The specified column must contain only "0" ans "1" characters. "0" is replaced by "1" and all the way around

char character	(	unsigned int	s,
		unsigned int	p
	)		const

inlinevirtual

Fast and unsecure accessor.

This accessor doesn't perform out-of-bound checking!

Parameters

s	the index of the sequence (line).
p	the position in the alignment (column).

Returns: The character at the given position.

Implements CharMatrix.

void clear ( )

virtual

Deletes all the content of the object.

Reimplemented from Container.

char get	(	unsigned int	sequence,
		unsigned int	position
	)		const

virtual

Gets a nucleotide.

This modifier does perform out-of-bound checking. The specified position must exist.

Parameters

sequence	the index of the sequence (line).
position	the position in the alignment (column).

Returns: the character at the given position.

Reimplemented from Container.

unsigned int ls ( ) const

virtual

Alignment length.

Returns 0 if the alignment is empty.

unsigned int ls ( unsigned int pos ) const

virtual

Length of a given sequence.

Calling this function is exactly the same as calling ls() (without arguments), regardless of the index provided, except that an exception is thrown if the index is out of bounds. Provided for compatibility with Container.

Parameters

pos	the index of the sequence.

Returns: the length of the alignment.

Reimplemented from Container.

unsigned int numberOfSequences ( ) const

inlinevirtual

Same as ns()

Implements CharMatrix.

unsigned int numberOfSites ( ) const

inlinevirtual

Same as ls()

Implements CharMatrix.

Align & operator= ( const Align & align )

Copy operator.

Align & operator= ( const Container & container )

Copy operator accepting a Container object.

All but the longest sequences are padded with ? to match the longest sequence's length.

unsigned int populationLabel ( unsigned int sequenceIndex ) const

inlinevirtual

Gets a group label (insecure)

Implements CharMatrix.

unsigned int remove ( unsigned int pos )

virtual

Removes a sequence from the alignment.

Parameters

pos	the index of the sequence to remove.

Returns: The new number of sequences.

Reimplemented from Container.

unsigned int removePosition ( unsigned int pos )

virtual

Removes a position (column) of the alignment.

Parameters

pos	the position to remove in the alignment.

Returns: The new length of the alignment.

void sequence	(	unsigned int	seq,
		const char *	sequence
	)

virtual

Replace a sequence string.

The new sequence must have the same length than the alignment. Otherwise, a EggUnalignedError is raised.

Parameters

seq	the index of the sequence to change.
sequence	the new sequence.

Reimplemented from Container.

virtual const char* sequence ( unsigned int pos ) const

inlinevirtual

Gets the name of a given sequence.

Parameters

pos	the index of the sequence.

Returns: The sequence string for that particular sequence.

Reimplemented from Container.

void set	(	unsigned int	sequence,
		unsigned	position,
		char	ch
	)

virtual

Sets a matrix position to a new character.

This modifier does perform out-of-bound checking. The specified position must exist.

Parameters

sequence	the index of the sequence (line).
position	the position in the alignment (column).
ch	the new character value.

Reimplemented from Container.

double sitePosition ( unsigned int position ) const

inlinevirtual

Just return the passed value.

Implements CharMatrix.

Align vslice ( std::vector< unsigned int > list_of_sites )

Extracts specified positions (columns) of the alignment.

All the specified sites are extracted in the specified order. This function is suitable for bootstrap (resample allowing redrawing the same site) and permutations.

This function doesn't perform out-of-bound checking.

Parameters

list_of_sites a vector containing alignment positions.

Returns: A copy of the object containing the specified set of positions.

Align vslice	(	unsigned int	a,
		unsigned int	b
	)

Extracts a range of positions (columns)

Parameters

a	the first position.
b	the index immediately passed the last sequence to extract.

Returns: A copy of the object containing the specified range of sequences.

Positions a to b-1 are extracted, provided that the indices fit in the current length of sequences. To extract all sequences, use align.vslice(0, align.ls()).

Note: invalid ranges will be silently supported. If a>=ls or b<=a, an empty object is returned. If b>ns, ls will be substituted to a.

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

/home/stephane/Documents/devel/egglib2/egglib-cpp/Align.hpp
/home/stephane/Documents/devel/egglib2/egglib-cpp/Align.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation