| Bioseq | Bio::SeqI implementing Object that queries a sequence in Chado instead of in memory. |
| Chromosome | Simple front end class to search and create Modware::Feature::CHROMOSOME objects. |
| Constant | Retrieves and caches commonly used ids and records from the database. |
| DBH | Global database connection object. Use for commits, rollbacks, custom SQL. |
| Feature | Base class for all Modware::Feature::* classes. Probably the most important class in Modware! |
| Gene | Convienent class to retrieve Modware::Feature::GENE objects. |
| Has_synonyms | Mixin class, provides accessor methods for classes tha have synonyms. |
| Iterator | An Iterator parent class inherited by the results returned from Modware::Search::* methods. |
| Protein_info | Results of many calculations based on protein sequence. |
| Root | Base class, provides common error handling methods. |
| Aligned | Parent Class of all Modware::Feature::* classes derived from BLAST alignments. |
| CHROMOSOME | Modware representation of a chromosome |
| CONTIG | Modware representation of a contig |
| EST | Modware representation of an EST (aligned) |
| GAP | Modware representation of a GAP |
| GENE | Modware representation of a gene |
| GENERIC | default Modware representation of a simple genome sequence feature (start, stop, strand) |
| MATCH | default Modware representation of an MATCH |
| MRNA | Modware representation of an mRNA |
| NCRNA | Modware representation of an ncRNA (non-coding RNA) |
| REFERENCE_FEATURE | Parent class for all features serving as coordinate system for other features (usually chromosome or contig) |
| Segment | Modware representation of arbitrary segment of some reference feature. |
| TRANSCRIPT | Parent class for all trnascript classes (mRNA, ncRNA, tRNA) |