GffFeatureReader.php
Reads a GFF3 annotation file into PlasmidFeature instances Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 6 October 2026
Table of Contents
Classes
- GffFeatureReader
- Deliberately independent of DatabaseParserFactory/ParseDbAbstractManager : that machinery is built around GenBank-style databases, each entry delimited by its own start/end sentinel line and ultimately persisted through Doctrine (DatabaseManager::recording()). GFF3 has neither shape - one feature per line, no entry delimiters, no persistence - and forcing it through that abstraction would fight it rather than reuse it. This class is a standalone, persistence-independent text reader, in keeping with the rest of Domain/Cloning.