Implement KEGG List Operation

[Rabadash8820]

The KEGG list operation will be implemented as a set of methods on our various KeggDb classes. We are moving away from the static operation class pattern because it makes a lot more sense to have operations be actions that a KeggDb instance can perform. Compare:

KeggList.InDatabase(PathwayDb.Instance)

vs

PathwayDb.Instance.ListPathways()

The second form is a bit more clean/fluent, and allows us to have very descriptive method names on each KeggDb class (ListModules(), ListCompounds(), etc.). Of course, this will require a little more dev effort, as we must implement the methods in each class, not some base abstract class.

Some notes on the List() methods:

• They will return a ListResults<ID> of all KeggIds in the KeggDb instance, where ID derives from KeggId.
• For each List() method, there should be one that returns all entries in a single massive list (very time- and memory-intensive), and one that returns them in a ListResults<T> data structure (faster and easier to get results a couple at a time
  • ListResults<T> will need to either inherit from Stream, or wrap a Stream
• EnzymeDb is the only composite databases that will have a List() method, returning a ListResults<TNumber> of all ECNumbers
• GenomeDb will have the following methods:
  • ListGenomeIds(): returns a ListResults<TNumber> of all genomes
  • ListOrganismCodes(): returns a ListResults<OrganismCode> of all organisms
  • ListGenesInGenome(TNumber): returns a ListResults<GeneId> of all genes in the provided genome
  • ListGenesInOrganism(OrganismCode): returns a ListResults<GeneId> of all genes belonging to the provided organism
• PathwayDb will have the following methods:
  • ListPathways: Returns a ListResults<MapNumber> of all KEGG Pathways
  • ListPathwaysInOrganism(OrganismCode): Returns a ListResults<MapNumber> of all pathways belonging to the provided organism
  • ListPathwaysInGenome(TNumber): Returns a ListResults<MapNumber> of all pathways belonging to the provided genome
• ModuleDb will have the following methods:
  • ListPathways: Returns a ListResults<MNumber> of all KEGG Modules
  • ListPathwaysInOrganism(OrganismCode): Returns a ListResults<MNumber> of all modules belonging to the provided organism
  • ListPathwaysInGenome(TNumber): Returns a ListResults<MNumber> of all modules belonging to the provided genome