| Aspects | A collection of global (enum) constants |
| DOMLight | Classes for generating and reading XML, based on DOM |
| GODiGraph | A directed graph representation of the Gene Ontology |
| GOError | Custom error logging |
| GOGraph | An unddirected unweighted graph representation of the Gene Ontology |
| GOGraphBase | A base class that all GO graph types inherit from |
| GOGrapher | |
| GOGrapher.Aspects | |
| GOGrapher.DOMLight | |
| GOGrapher.GODiGraph | |
| GOGrapher.GOError | |
| GOGrapher.GOGraph | |
| GOGrapher.GOGraphBase | |
| GOGrapher.GONode | |
| GOGrapher.GOProteinGraph | |
| GOGrapher.GOXDiGraph | |
| GOGrapher.GOXGraph | |
| GOGrapher.SteinerTree | |
| GOGrapher.Storage | |
| GOGrapher.Storage.FilebasedStorage | |
| GOGrapher.Storage.MysqlStorage | |
| GOGrapher.Storage.StorageInterface | |
| GOGrapher.StorageFactory | |
| GOGrapher.XGraphWeighters | |
| GOGrapher.XGraphWeighters.ICWeighter | |
| GOGrapher.XGraphWeighters.SimpleWeighter | |
| GOGrapher.XGraphWeighters.WeightingInterface | |
| GONode | Both node and term type vertice classes |
| GOProteinGraph | A graph that extends a GOGraph that will contain all of the gene products as vertices in a graph |
| GOXDiGraph | A weighted directed graph representation of the Gene Ontology |
| GOXGraph | A weighted undirected graph representation of the Gene Ontology |
| Storage | |
| Storage.DBStorage | Common storage classes/functions |
| Storage.FilebasedStorage | Storage is all in memory - The GO info is loaded from an owl file, and association files are specified for the associations that will be used |
| Storage.StorageInterface | Common storage classes/functions |
| StorageFactory | Singleton - makes storage mechanism |
| XGraphWeighters | |
| XGraphWeighters.InformationContent | A graph weighter that uses Information Content to assign weights to edges |
| XGraphWeighters.SimpleWeighter | A simple example of a weighting class - gives all edges a weight of 1 |
| XGraphWeighters.WeightingInterface | An interface that all graph weighters must implement |
1.5.6