Support local install of NCBI Taxonomy
fix NAMESPACE
typos
pull basic SQLite functions from rmisc
remove so and o files
fix dependency
return a proper NCBI defline for TSeqSets
fix NAMESPACE
getByRange methods for all Taxon objects with same return values; carry connection to local Taxonomy DB in all Taxon objects; make use of Constructor, Validator, and Show factory functions for list classes.
represent TaxonList as a Collection with shared database
fix variable in getTaxidByGeneID
is.na method for TaxonList
Classes for connections to taxon.db and geneid.db; pass connection objects to taxon constructors instead of paths; improve documentation
split createTaxonDB and createGeneidTB
fix NAMESPACE
bring naming scheme for getters in line with blastr
caching lineage data in an environment to speed up taxonomy queries
handle empty nodes in .lineage_to_cache
generalized caching
use memoisation to speed up queries