TOC for all levels

BioseqBio::SeqI implementing Object that queries a sequence in Chado instead of in memory.
ChromosomeSimple front end class to search and create Modware::Feature::CHROMOSOME objects.
ConstantRetrieves and caches commonly used ids and records from the database.
DBHGlobal database connection object. Use for commits, rollbacks, custom SQL.
FeatureBase class for all Modware::Feature::* classes. Probably the most important class in Modware!
GeneConvienent class to retrieve Modware::Feature::GENE objects.
Has_synonymsMixin class, provides accessor methods for classes tha have synonyms.
IteratorAn Iterator parent class inherited by the results returned from Modware::Search::* methods.
Protein_infoResults of many calculations based on protein sequence.
RootBase class, provides common error handling methods.

AlignedParent Class of all Modware::Feature::* classes derived from BLAST alignments.
CHROMOSOMEModware representation of a chromosome
CONTIGModware representation of a contig
ESTModware representation of an EST (aligned)
GAPModware representation of a GAP
GENEModware representation of a gene
GENERICdefault Modware representation of a simple genome sequence feature (start, stop, strand)
MATCHdefault Modware representation of an MATCH
MRNAModware representation of an mRNA
NCRNAModware representation of an ncRNA (non-coding RNA)
REFERENCE_FEATUREParent class for all features serving as coordinate system for other features (usually chromosome or contig)
SegmentModware representation of arbitrary segment of some reference feature.
TRANSCRIPTParent class for all trnascript classes (mRNA, ncRNA, tRNA)

Chromosomecollection of methods that return iterators of Modware::Feature::CHROMOSOME objects
Featurecollection of methods that return iterators of Modware::Feature::* objects
Genecollection of iterators that return iterators of Modware::Feature::GENE objects