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) |