Represents a multiple alignment. More...

#include <multiple_alignment.hh>

Inheritance diagram for LocARNA::MultipleAlignment:

Classes
class	AliColumn
	read only proxy class representing a column of the alignment More...
struct	AnnoType
	type of sequence annotation. enumerates legal annotation types More...
struct	FormatType
	file format type for multiple alignments More...
class	SeqEntry
	A row in a multiple alignment. More...
Public Types
typedef size_t	size_type
	size type
typedef std::vector< SeqEntry > ::const_iterator	const_iterator
	const iterator of sequence entries
Public Member Functions
	MultipleAlignment ()
	Construct empty.
	MultipleAlignment (const std::string &file, FormatType::type format=FormatType::CLUSTAL)
	Construct from file.
	MultipleAlignment (std::istream &in, FormatType::type format=FormatType::CLUSTAL)
	Construct from stream.
	MultipleAlignment (const std::string &name, const std::string &sequence)
	Construct as degenerate alignment of one sequence.
	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.
	MultipleAlignment (const Alignment &alignment, bool only_local=false, bool special_gap_symbols=false)
	Construct from Alignment object.
	MultipleAlignment (const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB)
	Construct from alignment edges and sequences.
virtual	~MultipleAlignment ()
	virtual destructor
const Sequence &	as_sequence () const
	"cast" multiple alignment to sequence
void	normalize_rna_symbols ()
	normalize rna symbols
size_type	num_of_rows () const
	Number of rows of multiple aligment.
bool	empty () const
	Emptiness check.
const SequenceAnnotation &	annotation (const AnnoType::type &annotype) const
	Read access of annotation by prefix.
void	set_annotation (const AnnoType::type &annotype, const SequenceAnnotation &annotation)
	Write access to annotation.
bool	has_annotation (const AnnoType::type &annotype) const
bool	is_proper () const
	Test whether alignment is proper.
pos_type	length () const
	Length of multiple aligment.
const_iterator	begin () const
	Begin for read-only traversal of name/sequence pairs.
const_iterator	end () const
	End for read-only traversal of name/sequence pairs.
bool	contains (const std::string &name) const
	Test whether name exists.
size_type	index (const std::string &name) const
	Access index by name.
const SeqEntry &	seqentry (size_type index) const
	Access name/sequence pair by index.
const SeqEntry &	seqentry (const std::string &name) const
	Access name/sequence pair by name.
size_type	deviation (const MultipleAlignment &ma) const
	Deviation of a multiple alignment from a reference alignment.
double	sps (const MultipleAlignment &ma, bool compalign=true) const
	Sum-of-pairs score between a multiple alignment and a reference alignment.
double	cmfinder_realignment_score (const MultipleAlignment &ma) const
	Cmfinder realignment score of a multiple alignment to a reference alignment.
double	avg_deviation_score (const MultipleAlignment &ma) const
	Average deviation score.
std::string	consensus_sequence () const
	Consensus sequence of multiple alignment.
AliColumn	column (size_type col_index) const
	Access alignment column.
void	append (const SeqEntry &seqentry)
	Append sequence entry.
void	prepend (const SeqEntry &seqentry)
	Prepend sequence entry.
void	operator+= (const AliColumn &c)
	Append a column.
void	operator+= (char c)
	Append the same character to each row.
void	reverse ()
	reverse the multiple alignment
std::ostream &	write (std::ostream &out, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write alignment to stream.
std::ostream &	write (std::ostream &out, size_t width, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write alignment to stream (wrapped)
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.
std::ostream &	write (std::ostream &out, size_type start, size_type end, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const
	Write sub-alignment to stream.
bool	checkAlphabet (const Alphabet< char > &alphabet) const
	check character constraints
void	write_debug (std::ostream &out=std::cout) const
	Print contents of object to stream.
Static Public Member Functions
static size_t	num_of_annotypes ()
	number of annotation types
Protected Member Functions
void	init (const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB, bool special_gap_symbols)
	Initialize from alignment edges and sequences.

Detailed Description

Represents a multiple alignment.

The multiple alignment is implemented as vector of name/sequence pairs.

Supports traversal of name/sequence pairs. The sequence entries support mapping from columns to positions and back.

Names are unique in a multiple alignment object.

Todo:: constructors ensure name uniqueness; if constructing as alignment of alignments, names are made unique if needed.

Sequences positions and column indices are 1..len.

MultipleAlignment can have anchor and structure annotation and can read and write them.

Note:: this class is agnostic of the type of sequences in the alignment; it does not check for 'allowed characters' nor transform characters. However, normalize_rna_bases() is provided to perform a normalization in the case of RNAs, which is generally assumed by the alignment engines and Vienna folding routines.

Todo:: because this class does not know whether it contains RNA, it would be useful to have a derived class RNAMultipleAlignment. This class could guarantee that its sequences are normalized RNA sequences. Consequently, we could enforce by the type system that RnaEnsemble is generated only from RNAMultipleAlignment etc.

Todo:: automatically adapt output width for sequence names to longest name

Constructor & Destructor Documentation

LocARNA::MultipleAlignment::MultipleAlignment	(	const std::string &	file,
		FormatType::type	format = `FormatType::CLUSTAL`
	)

Construct from file.

Parameters:

file	name of input file
format	file format (

See also:: FormatType)

Exceptions:

failure on read problems

See also:: MultipleAlignment(std::istream &in)

LocARNA::MultipleAlignment::MultipleAlignment	(	std::istream &	in,
		FormatType::type	format = `FormatType::CLUSTAL`
	)

Construct from stream.

Parameters:

in	input stream with alignment in clustalW-like format
format	file format (

See also:: FormatType)

Exceptions:

failure on read errors

LocARNA::MultipleAlignment::MultipleAlignment	(	const std::string &	name,
		const std::string &	sequence
	)

Construct as degenerate alignment of one sequence.

Parameters:

name	name of sequence
sequence	sequence strings

LocARNA::MultipleAlignment::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.

Parameters:

nameA	name of sequence A
nameB	name of sequence B
alistringA	alignment strings of sequence A
alistringB	alignment strings of sequence B

Note:: handling of gap-symbols: use same gap symbols as in given alistrings

LocARNA::MultipleAlignment::MultipleAlignment	(	const Alignment &	alignment,
		bool	only_local = `false`,
		bool	special_gap_symbols = `false`
	)

Construct from Alignment object.

Parameters:

alignment	object of type Alignment
only_local	if true, construct only local alignment
special_gap_symbols	if true, use special distinct gap symbols for gaps due to loop deletion '_' or sparsification '~'

Note:: Automatically computes a consensus anchor string if anchors are available. Consensus anchors containing duplicate names are cleared. Does not compute some kind of consensus structure, even if structure annotation of sequences A and B in Alignment is available.

LocARNA::MultipleAlignment::MultipleAlignment	(	const AlignmentEdges &	edges,
		const Sequence &	seqA,
		const Sequence &	seqB
	)

Construct from alignment edges and sequences.

Parameters:

edges	alignment edges
seqA	sequence A
seqB	sequence B

Note:: Automatically computes a consensus anchor string if anchors are available. Consensus anchors containing duplicate names are cleared. Does not compute some kind of consensus structure, even if structure annotation of sequences A and B is available.

Member Function Documentation

const SequenceAnnotation & LocARNA::MultipleAlignment::annotation ( const AnnoType::type & annotype ) const

Read access of annotation by prefix.

Parameters:

type	of annotation

Returns:: sequence annotation

Note:: returns ref to empty annotation if annotation is not available

void LocARNA::MultipleAlignment::append ( const SeqEntry & seqentry )

Append sequence entry.

Parameters:

seqentry new sequence entry

Precondition:: *this is empty or entry must have same size as *this

const Sequence & LocARNA::MultipleAlignment::as_sequence ( ) const

"cast" multiple alignment to sequence

Note:: this works like an upcast; this is ok, as long as sequence does not specify attributes

double LocARNA::MultipleAlignment::avg_deviation_score ( const MultipleAlignment & ma ) const

Average deviation score.

Parameters:

ma	multiple alignment

Returns:: average deviation fo alignment ma to reference alignment this

Precondition:: the sequences of ma have to occur in the alignment *this

Note:: this is not the same as deviation (and may be even not very similar)!

const_iterator LocARNA::MultipleAlignment::begin ( ) const [inline]

Begin for read-only traversal of name/sequence pairs.

Returns:: begin iterator

bool LocARNA::MultipleAlignment::checkAlphabet ( const Alphabet< char > & alphabet ) const

check character constraints

Check whether the alignment contains characters from the given alphabet only and, if warn, print warnings otherwise.

Parameters:

alphabet alphabet of admissible characters

Returns:: whether all characters are in the alphabet

double LocARNA::MultipleAlignment::cmfinder_realignment_score ( const MultipleAlignment & ma ) const

Cmfinder realignment score of a multiple alignment to a reference alignment.

Parameters:

ma	multiple alignment

Returns:: cmfinder realignment score of ma to reference alignment *this

Note:: this score was defined in Elfar Torarinsson, Zizhen Yao, Eric D. Wiklund, et al. Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res. 2008 (Section Realignment calculation)

Precondition:: the sequences of ma have to occur in the alignment *this

AliColumn LocARNA::MultipleAlignment::column ( size_type col_index ) const [inline]

Access alignment column.

Parameters:

col_index column index

Returns:: reference to alignment column with index i (1-based)

std::string LocARNA::MultipleAlignment::consensus_sequence ( ) const

Consensus sequence of multiple alignment.

Consensus sequence by simple majority in each column. Assume that only ascii < 127 characters occur

Returns:: consensus sequence as string

bool LocARNA::MultipleAlignment::contains ( const std::string & name ) const

Test whether name exists.

Parameters:

name	name of a sequence

Returns:: whether sequence with given name exists in multiple alignment

size_type LocARNA::MultipleAlignment::deviation ( const MultipleAlignment & ma ) const

Deviation of a multiple alignment from a reference alignment.

Parameters:

ma	multiple alignment

Returns:: deviation of ma from reference alignment *this deviation is defined for realignment in limited deviation from a reference alignment as preformed when --max-diff-aln is given with --max-diff to locarna.

Precondition:: the sequences of ma have to occur in the alignment *this

bool LocARNA::MultipleAlignment::empty ( ) const [inline]

Emptiness check.

Returns:: whether the object contains no sequences

Note:: an alignment containing one or more empty sequences is not empty in this sense.

const_iterator LocARNA::MultipleAlignment::end ( ) const [inline]

End for read-only traversal of name/sequence pairs.

Returns:: end iterator

bool LocARNA::MultipleAlignment::has_annotation ( const AnnoType::type & annotype ) const [inline]

Annotation availability

Parameters:

prefix annotation prefix

Returns:: wheter annotions with prefix are available

size_type LocARNA::MultipleAlignment::index ( const std::string & name ) const [inline]

Access index by name.

Precondition:: name exists

Parameters:

name	name of a sequence

Returns:: index of name/sequence pair with given name

void LocARNA::MultipleAlignment::init	(	const AlignmentEdges &	edges,
		const Sequence &	seqA,
		const Sequence &	seqB,
		bool	special_gap_symbols
	)		`[protected]`

Initialize from alignment edges and sequences.

Parameters:

edges	alignment edges
seqA	sequence A
seqB	sequence B
special_gap_symbols	if true, use special distinct gap symbols for gaps due to loop deletion '_' or sparsification '~'

bool LocARNA::MultipleAlignment::is_proper ( ) const

Test whether alignment is proper.

Returns:: whether all sequences have the same length

pos_type LocARNA::MultipleAlignment::length ( ) const [inline]

Length of multiple aligment.

Note:: Assumes proper alignment. Does not check, whether all sequences have the same length!

Returns:: length of first sequence in alignment

void LocARNA::MultipleAlignment::normalize_rna_symbols ( )

normalize rna symbols

See also:: normalize_rna_sequence()

Normalize the symbols in all aligned sequences assuming that they code for RNA

static size_t LocARNA::MultipleAlignment::num_of_annotypes ( ) [inline, static]

number of annotation types

Returns:: number of annotation types

size_type LocARNA::MultipleAlignment::num_of_rows ( ) const [inline]

Number of rows of multiple aligment.

Returns:: number of rows

void LocARNA::MultipleAlignment::operator+= ( const AliColumn & c )

Append a column.

Parameters:

c	column that is appended

void LocARNA::MultipleAlignment::operator+= ( char c )

Append the same character to each row.

Parameters:

c	character that is appended

void LocARNA::MultipleAlignment::prepend ( const SeqEntry & seqentry )

Prepend sequence entry.

Parameters:

seqentry new sequence entry

Precondition:: *this is empty or entry must have same size as *this

Note:: prepend is a lot more costly then append; it has cost linearly in the number of rows

const SeqEntry& LocARNA::MultipleAlignment::seqentry ( size_type index ) const [inline]

Access name/sequence pair by index.

Precondition:: index in range 0..size()-1

Parameters:

index index of name/sequence pair (0-based)

Returns:: sequence (including gaps) with given index

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

Access name/sequence pair by name.

Parameters:

name	name of name/sequence pair

Returns:: sequence (including gaps) with given name

void LocARNA::MultipleAlignment::set_annotation	(	const AnnoType::type &	annotype,
		const SequenceAnnotation &	annotation
	)		`[inline]`

Write access to annotation.

Parameters:

prefix	annotation prefix
annotation	sequence annotation

Todo:: check that annotation is valid for multiple alignment; throw failure if annotation is not valid

double LocARNA::MultipleAlignment::sps	(	const MultipleAlignment &	ma,
		bool	compalign = `true`
	)		const

Sum-of-pairs score between a multiple alignment and a reference alignment.

Parameters:

ma	multiple alignment
compalign	whether to compute score like compalign

Returns:: sum-of-pairs score of ma from reference alignment *this

Note:: Whereas the sps score for compalign==FALSE counts common matches only, the compalign score additionally counts common indels.

Precondition:: the sequences of ma have to occur in the alignment *this

std::ostream & LocARNA::MultipleAlignment::write	(	std::ostream &	out,
		FormatType::type	format = `MultipleAlignment::FormatType::CLUSTAL`
	)		const

Write alignment to stream.

Parameters:

out	output stream
format	alignment format; only CLUSTAL or STOCKHOLM; default: CLUSTAL (

See also:: FormatType)

Returns:: output stream

Writes one line "<name> <seq>" for each sequence; moereover, writes annotations.

Note:: does not write format header

std::ostream & LocARNA::MultipleAlignment::write	(	std::ostream &	out,
		size_t	width,
		FormatType::type	format = `MultipleAlignment::FormatType::CLUSTAL`
	)		const

Write alignment to stream (wrapped)

Parameters:

out	output stream
width	output stream
format	alignment format; only CLUSTAL or STOCKHOLM; default: CLUSTAL (

See also:: FormatType)

Returns:: output stream

Writes lines "<name> <seq>" per sequence, wraps lines at width

Note:: : do not write format header

std::ostream & LocARNA::MultipleAlignment::write	(	std::ostream &	out,
		size_type	start,
		size_type	end,
		FormatType::type	format = `MultipleAlignment::FormatType::CLUSTAL`
	)		const

Write sub-alignment to stream.

Write from position start to position end to output stream out; write lines "<name> <seq>"

Parameters:

out	output stream
start	start column (1-based)
end	end column (1-based)
format	alignment format; default: CLUSTAL (

See also:: FormatType)

Returns:: output stream

void LocARNA::MultipleAlignment::write_debug ( std::ostream & out = std::cout ) const

Print contents of object to stream.

Parameters:

out	output stream

std::ostream & LocARNA::MultipleAlignment::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.

The line is formatted such that it fits the output of the write methods.

Parameters:

out	output stream
name	name string
sequence	sequence string

Returns:: output stream

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

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation