Align module

Proposed align interface

inline void align(AlignRowConcept & vTarget, AlignRowConcept & hTarget, ContainerConcept const & vSource,  ContainerConcept const & hSource, ScoringConcept const & score, AlignConfig<Traits> const & config, ExecutionPolicy const & /*policy*/);
inline void align(Container<AlignRow>Concept & vTargets, Container<AlignRow>Concept & hTarget, ContainerOfContainerConcept const & vSources,  ContainerOfContainerConcept const & hSources, ScoringConcept const & score);

Alignment Traits

Possible Alignment Algorithms:

• GlobalAlignment + FreeEndGaps (add runtime option?) + LinearSpace (Hirschbergs variant)?
• LocalAlignment + SubOptimal | LinearSpace
• SplitAlingment + LinearSpace
• BandedChainAlignment + LinearSpace
• ExtendAlignment

Possible Traceback Options:

• NoTrace
• SingleTrace + GapsLeft | GapsRight
• FullTrace + GapsLeft | GapsRight

Possible Gap Options:

• LinearGaps
• AffineGaps
• DynamikGaps

Alignment Config

• Band parameters
• DPContext
• ScoutState

Execution Policies

• One-vs-One: Sequential | Parallel + Vectorised | Vectorised (AntiDiagonals)?
• Many-vs-Many: Vectorised
• One-vs-Many: Vectorised