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.
|
Modifier and Type | Method and Description |
---|---|
static void |
TaxonSQL.automaticUpdate(java.sql.Connection conn,
DBHelper helper,
TaxonFactory factory,
java.io.File delnodes,
java.io.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. |
Constructor and Description |
---|
Factory(SequenceBuilderFactory delegateFactory,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
java.lang.String sciNameKey,
java.lang.String commonNameKey,
java.lang.String ncbiTaxonKey) |
OrganismParser(SequenceBuilder delegate,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
java.lang.String sciNameKey,
java.lang.String commonNameKey,
java.lang.String ncbiTaxonKey)
Deprecated.
|
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 |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonParser.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
Deprecated.
Convert a stringified Taxon into a Taxon instance.
|
Taxon |
EbiFormat.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
Deprecated.
|