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

#include <sequence.hh>

Inheritance diagram for LocARNA::Sequence:

Collaboration diagram for LocARNA::Sequence:

Public Member Functions
	Sequence ()
	Construct empty.

	Sequence (const std::string &name, const std::string &sequence)
	Construct as single sequence. More...

AliColumn	operator[] (size_type col_index) const
	Access to columns. More...

std::vector< std::string >	names () const
	names vector (legacy, deprecated) More...

Public Member Functions inherited from LocARNA::MultipleAlignment
	MultipleAlignment ()
	Construct empty.

	MultipleAlignment (const std::string &file, FormatType::type format=FormatType::CLUSTAL)
	Construct from file. More...

	MultipleAlignment (std::istream &in, FormatType::type format=FormatType::CLUSTAL)
	Construct from stream. More...

	MultipleAlignment (const std::string &name, const std::string &sequence)
	Construct as degenerate alignment of one sequence. More...

	MultipleAlignment (const std::string &nameA, const std::string &nameB, const std::string &alistringA, const std::string &alistringB)
	Construct as pairwise alignment from names and alignment strings. More...

	MultipleAlignment (const Alignment &alignment, bool only_local=false, bool special_gap_symbols=false)
	Construct from Alignment object. More...

	MultipleAlignment (const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB)
	Construct from alignment edges and sequences. More...

virtual	~MultipleAlignment ()
	virtual destructor

const Sequence &	as_sequence () const
	"cast" multiple alignment to sequence More...

void	normalize_rna_symbols ()
	normalize rna symbols More...

size_type	num_of_rows () const
	Number of rows of multiple aligment. More...

bool	empty () const
	Emptiness check. More...

const SequenceAnnotation &	annotation (const AnnoType::type &annotype) const
	Read access of annotation by prefix. More...

void	set_annotation (const AnnoType::type &annotype, const SequenceAnnotation &annotation)
	Write access to annotation. More...

bool	has_annotation (const AnnoType::type &annotype) const

bool	is_proper () const
	Test whether alignment is proper. More...

pos_type	length () const
	Length of multiple aligment. More...

const_iterator	begin () const
	Begin for read-only traversal of name/sequence pairs. More...

const_iterator	end () const
	End for read-only traversal of name/sequence pairs. More...

bool	contains (std::string name) const
	Test whether name exists. More...

size_type	index (const std::string &name) const
	Access index by name. More...

const SeqEntry &	seqentry (size_type index) const
	Access name/sequence pair by index. More...

const SeqEntry &	seqentry (const std::string &name) const
	Access name/sequence pair by name. More...

size_type	deviation (const MultipleAlignment &ma) const
	Deviation of a multiple alignment from a reference alignment. More...

double	sps (const MultipleAlignment &ma, bool compalign=true) const
	Sum-of-pairs score between a multiple alignment and a reference alignment. More...

double	cmfinder_realignment_score (const MultipleAlignment &ma) const
	Cmfinder realignment score of a multiple alignment to a reference alignment. More...

double	avg_deviation_score (const MultipleAlignment &ma) const
	Average deviation score. More...

std::string	consensus_sequence () const
	Consensus sequence of multiple alignment. More...

AliColumn	column (size_type col_index) const
	Access alignment column. More...

void	append (const SeqEntry &seqentry)
	Append sequence entry. More...

void	prepend (const SeqEntry &seqentry)
	Prepend sequence entry. More...

void	operator+= (const AliColumn &c)
	Append a column. More...

void	operator+= (char c)
	Append the same character to each row. More...

void	reverse ()
	reverse the multiple alignment

std::ostream &	write (std::ostream &out, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write alignment to stream. More...

std::ostream &	write (std::ostream &out, size_t width, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write alignment to stream (wrapped) More...

std::ostream &	write_name_sequence_line (std::ostream &out, const std::string &name, const std::string &sequence, size_t namewidth) const
	Write formatted line of name and sequence. More...

std::ostream &	write (std::ostream &out, size_type start, size_type end, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write sub-alignment to stream. More...

bool	checkAlphabet (const Alphabet< char > &alphabet) const
	check character constraints More...

void	write_debug (std::ostream &out=std::cout) const
	Print contents of object to stream. More...

Additional Inherited Members
Public Types inherited from LocARNA::MultipleAlignment
typedef size_t	size_type
	size type

typedef std::vector< SeqEntry >::const_iterator	const_iterator
	const iterator of sequence entries

Static Public Member Functions inherited from LocARNA::MultipleAlignment
static size_t	num_of_annotypes ()
	number of annotation types More...

Protected Member Functions inherited from LocARNA::MultipleAlignment
void	init (const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB, bool special_gap_symbols)
	Initialize from alignment edges and sequences. More...

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

name	name of sequence
sequence	sequence 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_index column 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:

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation