Handles a set of sequence alignment (aligned or not) More...

#include <Container.hpp>

Inheritance diagram for Container:

Public Member Functions
	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	clear ()
	Clears all content of the object. More...

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

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

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

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

virtual void	appendSequence (unsigned int pos, const char *sequence)
	Appends a string to the a given sequence. More...

virtual void	set (unsigned int sequence, unsigned position, char ch)
	Changes a character. More...

virtual char	get (unsigned int s, unsigned int p) const
	Gets a given character. 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 unsigned int	ls (unsigned int pos) const
	Gets the length of a given sequence. More...

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

virtual const char *	sequence (unsigned int pos) const
	Gets the name of 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	setFromSource (unsigned int number_of_sequences, const char const const cstring_array)

virtual void	copyObject (const Container &)

virtual void	getNamesAndGroups (const Container &)

Protected Attributes
unsigned int	_ns

unsigned int *	lnames

char **	names

char **	sequences

unsigned int *	groups

Detailed Description

Handles a set of sequence alignment (aligned or not)

Creation from a file or string stream should be performed using the class Fasta.

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 Container was a list of triplets (name, sequence, group).

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

Constructor & Destructor Documentation

Container ( )

Creates an empty object.

Container ( const Container & source )

Copy constructor.

Container	(	unsigned int	number_of_sequences,
		char const const const	cstring_array
	)

Creates an object from a data matrix.

Allows you to create an object from data stored in a char* array. The array's size must be passed to the constructor. Since sequences can have different lengths, you need to terminate each sequence by a NULL character. This constructor is dedicated to very performance-critical tasks. For usual tasks, using the default constructor and subsequently adding sequences with addSeq should be enough.

Parameters

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

~Container ( )

virtual

Destructor.

Member Function Documentation

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

virtual

Adds a sequence to the object.

Parameters

name	the name of the sequence, as a c-string.
sequence	the sequence string, as a c-string.
group	the group index of the sequence.

Returns: The new number of sequences.

Reimplemented in Align.

void appendSequence	(	unsigned int	pos,
		const char *	sequence
	)

virtual

Appends a string to the a given sequence.

Parameters

pos	the sequence index.
sequence	the sequence to append at the end of the current one.

Reimplemented in Align.

void clear ( )

virtual

Clears all content of the object.

Reimplemented in Align.

unsigned int equalize ( char ch = '?' )

Equalizes sequence lengths.

Extends sequences as need to ensure that all sequences have the same length.

Parameters

ch	the character to use for padding.

Returns: The final length obtained, which is the length of the longest sequence before the operation.

int find	(	const char *	string,
		bool	strict = `true`
	)		const

Finds a sequence by its name.

Gets the position of the first sequence with the specified name.

Parameters

string	a sequence name.
strict	if true, seeks an exact match. If false, compares only until the end of the requested name (for example: ATCFF will match ATCFF_01 if strict is false).

Returns: The lowest index where the name matches, -1 if no sequence has such name.

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

virtual

Gets a given character.

Parameters

s	the sequence index.
p	the character index.

Returns: the character value.

The positions must fit in the current ranges.

Reimplemented in Align.

void group	(	unsigned int	pos,
		unsigned int	group
	)

virtual

Changes the group index of a given sequence.

Parameters

pos	the sequence index.
group	the new group index value.

unsigned int group ( unsigned int pos ) const

virtual

Gets the group index of a given sequence.

Parameters

pos	the index of the sequence.

Returns: The group index of that particular sequence.

Container hslice	(	unsigned int	a,
		unsigned int	b
	)		const

Extracts a range of sequences.

Parameters

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

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

Sequences a to b-1 are extracted, provided that the indices fit in the current number of sequences. To extract all sequences, use container.hslice(0, container.ns()).

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.

bool isEqual ( ) const

Checks if all lengths are equal.

Returns true if the length of all sequences are equal or if there is less thant two sequences.

unsigned int ls ( unsigned int pos ) const

virtual

Gets the length of a given sequence.

Parameters

pos	the index of the sequence.

Returns: The length of that particular sequence.

Reimplemented in Align.

void name	(	unsigned int	pos,
		const char *	name
	)

virtual

Changes the name of a given sequence.

Parameters

pos	the sequence index.
name	the new name as a C-like string.

const char * name ( unsigned int pos ) const

virtual

Gets the name of the a given sequence.

Parameters

pos	the index of the sequence.

Returns: The name of that particular sequence.

unsigned int ns ( ) const

Gets the number of sequences.

Container & operator= ( const Container & source )

Assignment operator.

unsigned int remove ( unsigned int pos )

virtual

Removes a sequence from the object.

Parameters

pos	the index of the sequence to remove.

Returns: The new number of sequences.

Reimplemented in Align.

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

virtual

Changes the sequence string of a given sequence.

Parameters

pos	the sequence index.
sequence	the new sequence as a C-like string.

Reimplemented in Align.

const char * sequence ( unsigned int pos ) const

virtual

Gets the name of a given sequence.

Parameters

pos	the index of the sequence.

Returns: The sequence string for that particular sequence.

Reimplemented in Align.

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

virtual

Changes a character.

Parameters

sequence	the sequence index.
position	the character index.
ch	the new character value.

The positions must fit in the current ranges.

Reimplemented in Align.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation