Interfaces
Table of Contents
Interfaces
- BedFeatureReaderInterface
- Interface BedFeatureReaderInterface - reads a BED annotation file into PlasmidFeature instances,
independently of any specific Plasmid.
- BedFeatureWriterInterface
- Interface BedFeatureWriterInterface - the inverse of BedFeatureReaderInterface : serializes
PlasmidFeature instances into BED text.
- FeatureOverlapInterface
- Interface FeatureOverlapInterface - answers "does this restriction site fall inside that CDS ?" and
"do these two annotations overlap ?" for the features of a circular Plasmid, correctly handling a
feature that crosses the origin.
- GenbankPlasmidMapperInterface
- Interface GenbankPlasmidMapperInterface - transforms an already-parsed GenBank record into a
Plasmid, controlled and reversible, never touching the parser itself.
- GenbankWriterInterface
- Interface GenbankWriterInterface - serializes a Plasmid into GenBank flat-file text. The
counterpart of GenbankPlasmidMapper, not of ParseGenbankManager directly : it writes a Plasmid
aggregate, not the raw Feature entities the legacy parser produces.
- GffFeatureReaderInterface
- Interface GffFeatureReaderInterface - reads a GFF3 annotation file into PlasmidFeature instances,
independently of any specific Plasmid.
- GffFeatureWriterInterface
- Interface GffFeatureWriterInterface - the inverse of GffFeatureReaderInterface : serializes
PlasmidFeature instances into GFF3 text.
- GibsonAssemblyInterface
- Interface GibsonAssemblyInterface - answers "do these two fragments already share the homology a
Gibson junction needs ?" and, when they do not, designs the primer tails that would give them one.
- LinearRestrictionDigestInterface
- Interface LinearRestrictionDigestInterface - computes where a set of restriction enzymes of any
family (II, IIb, IIs) cut a linear DNA sequence, and the fragments that digestion produces. The
counterpart of RestrictionDigestInterface, which digests a circular Plasmid.
- PlasmidRecordMapperInterface
- Interface PlasmidRecordMapperInterface - converts between the immutable Plasmid aggregate and its
Doctrine storage shape, so the aggregate never has to be a Doctrine entity itself.
- RestrictionDigestInterface
- Interface RestrictionDigestInterface - computes where a set of restriction enzymes cut a circular
Plasmid, and the fragments that digestion produces.
- RestrictionEndCompatibilityInterface
- Interface RestrictionEndCompatibilityInterface - decides whether two restriction ends can be
ligated together.