LocARNA::Sequence Class Reference

"Sequence View" of multiple alignment as array of column vectors More...

#include <sequence.hh>

Inheritance diagram for LocARNA::Sequence:

List of all members.

Public Member Functions
	Sequence ()
	Construct empty.
	Sequence (const std::string &name, const std::string &sequence)
	Construct as single sequence.
AliColumn	operator[] (size_type col_index) const
	Access to columns.
std::vector< std::string >	names () const
	names vector (legacy, deprecated)

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Detailed Description

"Sequence View" of multiple alignment as array of column vectors

Note:

use MultipleAlignment::as_sequence() to 'convert' from MultipleAlignment to Sequence.

the conceptual relation between Sequence and MultipleAlignent is that the two classes are equivalent views of a multiple alignment. Therefore, casting between both should be free of cost, in particular for references! operator [] is supported, depending on the static type, only for Sequence. There should be a way to expresse this relation in a nicer way.

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Constructor & Destructor Documentation

LocARNA::Sequence::Sequence	(	const std::string &	name,
		const std::string &	sequence
	)		[inline]

Construct as single sequence.

Parameters:

name	name of sequence
sequence	sequence string

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Member Function Documentation

std::vector< std::string > LocARNA::Sequence::names

(

)

const

names vector (legacy, deprecated)

Returns:

vector of sequence names

Note:

deprecated: in place of names()[i], rather use seqentry(i).name()

AliColumn LocARNA::Sequence::operator[]

(

size_type

col_index

)

const [inline]

Access to columns.

Parameters:

col_index

column index

Returns:

alignment column (proxy class)

Note:

allows array notation via [] operator; this is the main difference to MultipleAlignment class

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

• src/LocARNA/sequence.hh
• src/LocARNA/sequence.cc