ValueObject
Table of Contents
Classes
- FeatureOverlap
- Order is not meaningful : getFirst()/getSecond() simply mirror the order the two features were
found in, not any priority between them.
- FeatureType
- Class FeatureType - the minimal set of annotation kinds a cloning plasmid needs. The model never
infers one of these from a feature's name; the caller (or, later, GenbankPlasmidMapper) decides.
- GibsonHomologyArms
- Both tails are given 5' -> 3', ready to be prepended to the primer's own annealing portion (this
class only designs the homology arm, not the annealing portion itself, which needs its own melting
temperature calculation). downstreamForwardPrimerTail goes on the forward primer that amplifies the
downstream fragment ; upstreamReversePrimerTail goes on the reverse primer that amplifies the
upstream fragment. Each tail carries one share of the overlap : after PCR, the two products share
the downstream forward tail followed by the reverse complement of the upstream reverse tail, which
is what lets Gibson assembly's exonuclease chew-back and annealing join them. A 1-base overlap
leaves the upstream reverse tail empty.
- PlasmidFeature
- Coordinates are 1-based inclusive, the convention used by GenBank and EMBL feature tables. Start
and end are only validated to be at least 1 here : since a lone feature does not know the length
of the plasmid it will belong to, the upper bound is checked by Plasmid when the feature is
attached. A start strictly greater than end is valid and means the feature crosses the origin.
- RestrictionCut
- All positions are zero-based, consistently with CircularDnaSequence, and already wrapped within
[0, plasmid length[. recognitionPosition is where the enzyme's recognition pattern was matched;
upperCutPosition and lowerCutPosition are the boundary positions where the upper and lower strands
are actually severed, which may differ from recognitionPosition for enzymes cutting outside their
own recognition sequence (Type IIb and IIs). reverseStrand tells whether the recognition sequence
was found on the plasmid's own reference strand (false) or only detectable as its reverse
complement, i.e. the enzyme actually binds the other strand (true) ; upperCutPosition and
lowerCutPosition are always expressed in the reference strand's coordinates either way.
- RestrictionEnd
- The overhang sequence, when there is one, is always given as the top-strand bases spanning the
upper and lower cut positions, read 5' -> 3' on the strand the cut positions were computed from.
- RestrictionFragment
- Class RestrictionFragment
- Strand
- Class Strand