LocARNA::SequenceAnnotation Class Reference

Annotation of a sequence. More...

#include <sequence_annotation.hh>

Public Member Functions
	SequenceAnnotation (size_type name_length=0)
	Construct empty. More...
	SequenceAnnotation (const std::string &annotation_string)
	Construct single string. More...
	SequenceAnnotation (const std::vector< std::string > &annotation_strings)
	Construct from vector of strings. More...
	SequenceAnnotation (const AlignmentEdges &edges, const SequenceAnnotation &annotationA, const SequenceAnnotation &annotationB)
	Construct as consensus annotation. More...
size_t	length () const
	Size of the represented range. More...
bool	empty () const
	Check empty. More...
size_t	name_length () const
	Name length. More...
const std::string &	annotation_string (size_t i) const
std::string	single_string (char sep='#') const
bool	is_neutral_pos (size_t i) const
	Test neutral name at a position. More...
std::string	name (size_t i) const
	Access name at position. More...
void	push_back_name (const name_t &name)
	Push back name to the annotation strings in annotation_. More...
bool	duplicate_names () const

Static Public Member Functions
static const SequenceAnnotation &	empty_instance ()
	initialize the static member empty_instance
static bool	is_neutral_char (char c)
	Test for neutral character. More...
static bool	is_neutral (const name_t &name)
	Test neutral name. More...
static bool	clashing_names (const AlignmentEdges &edges, const SequenceAnnotation &annotationA, const SequenceAnnotation &annotationB)

Detailed Description

Annotation of a sequence.

Defines names for positions from 1..size; allows construct as consensus of two aligned annotation sequences.

Constructor & Destructor Documentation

LocARNA::SequenceAnnotation::SequenceAnnotation ( size_type  name_length = 0 )

inlineexplicit

Construct empty.

Parameters

name_length

length of names

LocARNA::SequenceAnnotation::SequenceAnnotation ( const std::string &  annotation_string )

explicit

Construct single string.

Parameters

annotation_string

string of '#'-separated sub-strings

LocARNA::SequenceAnnotation::SequenceAnnotation ( const std::vector< std::string > &  annotation_strings )

explicit

Construct from vector of strings.

Parameters

annotation_strings

vector of annotation strings

The strings specify names of uniform length. The name of a position i is the string annotation_strings[0][i]+...+annotation_strings[k-1][i], where k=annotation_strings.size()

LocARNA::SequenceAnnotation::SequenceAnnotation	(	const AlignmentEdges &	edges,
		const SequenceAnnotation &	annotationA,
		const SequenceAnnotation &	annotationB
	)

Construct as consensus annotation.

Parameters

edges	alignment edges between A and B
annotationA	annotation A
annotationB	annotation B

Returns

consensus annotation of A and B

Note

If two different names are aligned (name clash!), the lexicographically smaller name is selected to resolve the conflict

If two equal names are not aligned, this can result in duplicate names in the consensus

The consensus contains all names that appear in either A or B or both at the position of the corresponding alignment edge.

Precondition

names in annotationA and annotationB must have the same lengths

Member Function Documentation

const std::string& LocARNA::SequenceAnnotation::annotation_string ( size_t  i ) const

inline

Access to annotation strings

Parameters

i	index; 0-based

Returns

annotation string with index i

bool LocARNA::SequenceAnnotation::empty ( ) const

inline

Check empty.

Returns

whether empty

bool LocARNA::SequenceAnnotation::is_neutral ( const name_t &  name )

static

Test neutral name.

Returns

whether name is neutral, i.e. contains no non-neutral characters

static bool LocARNA::SequenceAnnotation::is_neutral_char ( char  c )

inlinestatic

Test for neutral character.

Parameters

c

Returns

whether c is neutral

bool LocARNA::SequenceAnnotation::is_neutral_pos

(

size_t

i

)

const

Test neutral name at a position.

Parameters

i	position of name

Returns

whether name at position i is neutral, i.e. contains no non-neutral characters

size_t LocARNA::SequenceAnnotation::length ( ) const

inline

Size of the represented range.

Returns

size, where represented range of positions is 1..size

std::string LocARNA::SequenceAnnotation::name

(

size_t

i

)

const

Access name at position.

Parameters

i

position

Returns

name at position i

size_t LocARNA::SequenceAnnotation::name_length ( ) const

inline

Name length.

Returns

length of names

void LocARNA::SequenceAnnotation::push_back_name

(

const name_t &

name

)

Push back name to the annotation strings in annotation_.

Parameters

name

Name

std::string LocARNA::SequenceAnnotation::single_string

(

char

sep = '#'

)

const

Annotation description as single string

Parameters

sep	separator between annotation strings

Returns

string of annotation strings separated by sep

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

• src/LocARNA/sequence_annotation.hh
• src/LocARNA/sequence_annotation.cc