LocARNA::MultipleAlignment::SeqEntry Class Reference

A row in a multiple alignment. More...

#include <multiple_alignment.hh>

List of all members.

Public Types
typedef MultipleAlignment::size_type	size_type
	size type
typedef std::pair< pos_type, pos_type >	pos_pair_t
	pair of positions
Public Member Functions
	SeqEntry (const std::string &name, const std::string &seq)
	Construct from strings name and seq.
	SeqEntry (const std::string &name, const string1 &seq)
	Construct from strings name and 1-based string seq.
	SeqEntry (const std::string &name, const std::string &description, const std::string &seq)
	Construct from strings name, description and seq.
	SeqEntry (const std::string &name, const std::string &description, const string1 &seq)
	Construct from strings name, description and 1-based string seq.
const std::string &	name () const
	(read-only) access to name
const std::string &	description () const
	(read-only) access to description
const string1 &	seq () const
	(read-only) access to seq
size_type	length_wogaps () const
	length without gaps
pos_type	pos_to_col (pos_type pos) const
	map sequence position -> alignment column.
pos_pair_t	col_to_pos (pos_type col) const
void	reverse ()
	reverse sequence
void	push_back (char c)
	append character to sequence
void	set_seq (const string1 &seq)
	write access to seq

---

Detailed Description

A row in a multiple alignment.

pair of a name string and a sequence string; support projections

See also:

MultipleAlignment

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Constructor & Destructor Documentation

LocARNA::MultipleAlignment::SeqEntry::SeqEntry	(	const std::string &	name,
		const std::string &	seq
	)		[inline]

Construct from strings name and seq.

Parameters:

name	Sequence name
seq	Sequence string

Note:

empty description

LocARNA::MultipleAlignment::SeqEntry::SeqEntry	(	const std::string &	name,
		const string1 &	seq
	)		[inline]

Construct from strings name and 1-based string seq.

Parameters:

name	Sequence name
seq	Sequence string

Note:

empty description

LocARNA::MultipleAlignment::SeqEntry::SeqEntry	(	const std::string &	name,
		const std::string &	description,
		const std::string &	seq
	)		[inline]

Construct from strings name, description and seq.

Parameters:

name	Sequence name
description	Sequence description
seq	Sequence string

LocARNA::MultipleAlignment::SeqEntry::SeqEntry	(	const std::string &	name,
		const std::string &	description,
		const string1 &	seq
	)		[inline]

Construct from strings name, description and 1-based string seq.

Parameters:

name	Sequence name
description	Sequence description
seq	Sequence string

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Member Function Documentation

MultipleAlignment::SeqEntry::pos_pair_t LocARNA::MultipleAlignment::SeqEntry::col_to_pos

(

pos_type

col

)

const

map alignment column -> sequence positions

Note:

time O(len)

Parameters:

col	column index in aligmnent

Returns:

pair of positions (pos1,pos2) if column col contains a non-gap, then pos1=pos2 is the position of the gap if column col contains a gap, then pos1 is the sequence position left of the gap or 0 and pos2 the position right of the gap or sequence length+1

size_type LocARNA::MultipleAlignment::SeqEntry::pos_to_col

(

pos_type

pos

)

const

map sequence position -> alignment column.

Note:

time O(len)

Parameters:

pos	position in sequence (without gaps) as marginal cases: pos 0 maps to 0 and a too large position maps to length+1

void LocARNA::MultipleAlignment::SeqEntry::push_back

(

char

c

)

[inline]

append character to sequence

Parameters:

c

character

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

• src/LocARNA/multiple_alignment.hh
• src/LocARNA/multiple_alignment.cc