Simple dynamic programming alignment. More...

Classes
class	shore::dp_alignment_matrix
	Matrix representation of an alignment. More...

struct	shore::dp_traits< RefType, QryType >
	Dynamic programming type traits. More...

struct	shore::dp_traits< shore::nuc::base, shore::nuc::base >
	Dynamic programming type traits for shore::nuc::base. More...

struct	shore::dp_alignment< RefIter, QryIter, Scoring >
	Representation of a dynamic programming alignment. More...

struct	shore::dp_aligner_config
	Configuration for dp_aligner_pipe. More...

class	shore::dp_aligner_pipe< RefIter, QryIter, Scoring >
	Dynamic programming aligner. More...

class	shore::dp_multialigner_pipe< RefIter, QryIter, Scoring >
	Dynamic programming aligner (multiple reference sequences). More...

struct	shore::dp_trace
	Dynamic programming alignment backtrace. More...

struct	shore::dp_backtracer_config
	Dynamic programming alignment backtracer configuration. More...

class	shore::dp_backtracer_pipe< RefIter, QryIter, Scoring, AlnBuilder >
	Dynamic programming alignment backtracer class. More...

Typedefs
typedef shore::pipe_box < dp_mapper_pipe >	shore::dp_mapper

typedef shore::sink < dp_mapping_writer >	shore::dp_mapping_sink

Enumerations
enum	shore::AlignmentMode { ALN_NONE =-1, ALN_GLOBAL =0, ALN_DANGLING_REF =1, ALN_DANGLING_QRY =2, ALN_DANGLING_ANY =3, ALN_LOCAL =7 }
	Valid ways of aligning one end of the sequences.

Functions
template<typename RefIter , typename QryIter , typename Scoring >
void	shore::dp_align (dp_alignment_matrix &matrix, RefIter rbeg, const size_t rsize, QryIter qbeg, const size_t qsize, const Scoring scoring, const AlignmentMode left_ends, const AlignmentMode exclude_left=ALN_NONE, const AlignmentMode exclude_right=ALN_NONE)
	Perform dynamic programming alignment.

Detailed Description

Simple dynamic programming alignment.

Classes