LocARNA-1.9.2
 All Classes Files Functions Variables Typedefs Enumerations Enumerator Friends
Public Member Functions
LocARNA::Sequence Class Reference

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

#include <sequence.hh>

Inheritance diagram for LocARNA::Sequence:
LocARNA::MultipleAlignment

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)

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.

Constructor & Destructor Documentation

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

Construct as single sequence.

Parameters:
namename of sequence
sequencesequence string

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_indexcolumn index
Returns:
alignment column (proxy class)
Note:
allows array notation via [] operator; this is the main difference to MultipleAlignment class

The documentation for this class was generated from the following files:
 All Classes Files Functions Variables Typedefs Enumerations Enumerator Friends