LocARNA::AnchorConstraints Class Reference

Represents anchor constraints between two sequences. More...

#include <anchor_constraints.hh>

Public Types
typedef size_t	size_type
	size type
typedef std::pair< size_type, size_type >	size_pair_t
	size pair
typedef size_pair_t	range_t
	type of range
typedef std::vector< range_t >	range_seq_t
	type for sequence of ranges

Public Member Functions
	AnchorConstraints (size_type lenA, const std::vector< std::string > &seqCA, size_type lenB, const std::vector< std::string > &seqCB)
	Construct from sequence lengths and anchor names. More...
	AnchorConstraints (size_type lenA, const std::string &seqCA, size_type lenB, const std::string &seqCB)
	Construct from sequence lengths and anchor names. More...
bool	allowed_edge (size_type i, size_type j) const
int	match_to_a (size_type i) const
int	match_to_b (size_type i) const
bool	aligned_in_a (size_type i) const
	is position i in sequence A aligned to any position in B
bool	aligned_in_b (size_type j) const
	is position j in sequence B aligned to any position in A
std::string	get_name_a (size_type i) const
	get the name of position i in A
std::string	get_name_b (size_type j) const
	get the name of position j in B
size_type	name_size () const
	returns length/size of the names
bool	empty () const
	is the constraint declaration empty
size_pair_t	rightmost_anchor () const
	return the positions (i,j) of the rightmost anchor constraint
size_pair_t	leftmost_anchor () const
	return the positions (i,j) of the leftmost anchor constraint

Detailed Description

Represents anchor constraints between two sequences.

Maintains the constraints on (non-structural) alignment edges that have to be satisfied during the alignment

Constructor & Destructor Documentation

LocARNA::AnchorConstraints::AnchorConstraints	(	size_type	lenA,
		const std::vector< std::string > &	seqCA,
		size_type	lenB,
		const std::vector< std::string > &	seqCB
	)

Construct from sequence lengths and anchor names.

Parameters

lenA	length of sequence A
seqCA	vector of anchor strings for sequence A
lenB	length of sequence B
seqCB	vector of anchor strings for sequence B

The constraints (=alignment edges that have to be satisfied) are encoded as follows: equal symbols in the sequences for A and B form an edge

In order to specify an arbitrary number of sequences, the strings can consist of several lines, then a symbol consists of all characters of the column. '.' and ' ' are neutral character, in the sense that columns consisting only of neutral characters do not specify names that have to match. However, neutral characters are not identified in names that contain at least one non-neutral character!

Example: seqCA={"..123...."} seqCB={"...12.3...."}

specifies the edges (3,4), (4,5), and (5,7)

Example 2: seqCA={"..AAB....", "..121...."} seqCB={"...AA.B....", "...12.1...."} specifies the same constraints, allowing a larger name space for constraints.

LocARNA::AnchorConstraints::AnchorConstraints	(	size_type	lenA,
		const std::string &	seqCA,
		size_type	lenB,
		const std::string &	seqCB
	)

Construct from sequence lengths and anchor names.

Parameters

lenA	length of sequence A
seqCA	concatenated anchor strings for sequence A (separated by '#')
lenB	length of sequence B
seqCB	concatenated anchor strings for sequence B (separated by '#')

for semantics of anchor strings see first constructor

Member Function Documentation

bool LocARNA::AnchorConstraints::allowed_edge ( size_type  i, size_type  j  ) const

inline

is the alignment edge i~j (i.e. the match of i and j) allowed? an alignment edge is allowed, iff it is not in conflict with any anchor constraint

int LocARNA::AnchorConstraints::match_to_a ( size_type  i ) const

inline

matching position in b for position i in a

Parameters

i	position in sequence A

Returns

j, 1<=j<=lenB, if there is an anchor from A_i to B_j, 0 if there is no name for position i in A, and -1 if there is a name for A_i, but no match to B

int LocARNA::AnchorConstraints::match_to_b ( size_type  i ) const

inline

matching position in b for position i in a

Parameters

i	position in sequence B

Returns

j

See also

match_to_a

---

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

• src/LocARNA/anchor_constraints.hh
• src/LocARNA/anchor_constraints.cc