Uses of Interface
org.biojava.bio.taxa.TaxonFactory

Packages that use TaxonFactory

Package	Description
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.taxa	Taxonomy object for representing species information.

Uses of TaxonFactory in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql with parameters of type TaxonFactory

Modifier and Type	Method and Description
static void	TaxonSQL.automaticUpdate(Connection conn, DBHelper helper, TaxonFactory factory, File delnodes, File merged) Deprecated. This method tries to perform a complete update according to the given TaxonFactory, which already contains the newes taxa and the files available at the NCBI-FTP-Site.

Uses of TaxonFactory in org.biojava.bio.seq.io

Constructors in org.biojava.bio.seq.io with parameters of type TaxonFactory

Constructor and Description
OrganismParser.Factory(SequenceBuilderFactory delegateFactory, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey)
OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey) Deprecated.

Uses of TaxonFactory in org.biojava.bio.taxa

Classes in org.biojava.bio.taxa that implement TaxonFactory

Modifier and Type	Class and Description
class	SimpleTaxonFactory Deprecated. replaced by classes in org.biojavax.bio.taxa
class	WeakTaxonFactory Deprecated. replaced by classes in org.biojavax.bio.taxa

Methods in org.biojava.bio.taxa with parameters of type TaxonFactory

Modifier and Type	Method and Description
Taxon	TaxonParser.parse(TaxonFactory taxonFactory, String taxonString) Deprecated. Convert a stringified Taxon into a Taxon instance.
Taxon	EbiFormat.parse(TaxonFactory taxonFactory, String taxonString) Deprecated.