Result
Table of Contents
Classes
- BedImportResult
- Unlike GenbankImportResult, this never wraps a whole Plasmid : a BED file annotates a sequence it
does not itself carry, exactly like GffImportResult ; the caller attaches getFeatures() onto a
Plasmid it already has.
- GenbankImportResult
- The mapping always either succeeds with a Plasmid (skipping any feature it could not represent) or
throws (for an unsupported topology) ; getWarnings() lists every feature that was skipped and why,
so nothing is ever silently dropped without being reported.
- GffImportResult
- Unlike GenbankImportResult, this never wraps a whole Plasmid : a GFF3 file annotates a sequence it
does not itself carry, so the caller is expected to attach getFeatures() onto a Plasmid it already
has, via repeated withFeature() calls, which is also where an out-of-range coordinate for that
particular plasmid would surface.
- GibsonJunctionResult
- hasOverlap() is false, and getOverlapLength()/getOverlapSequence() are 0/null, when no exact match
of at least the requested minimum length was found at the junction - a legitimate, expected outcome
for a junction that still needs primer tails designed (see GibsonAssemblyManager::designHomologyArms()),
not an error.
- LinearRestrictionDigestResult
- getCuts() lists every recognition site that cuts inside the sequence, including several
isoschizomers cutting at the same position ; getFragments() lists the distinct fragments, from
the left end of the sequence to its right end, so n distinct cut positions give n + 1 of them.
- RestrictionDigestResult
- getCuts() lists every recognition site found, including several isoschizomers cutting at the same
position; getFragments() lists the distinct linear fragments that digest actually produces, so its
count only ever equals the number of distinct cut positions, never the number of raw cuts.