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.
|
static int |
TaxonSQL.putTaxon(java.sql.Connection conn,
DBHelper helper,
Taxon taxon) |
Deprecated.
Adds a Taxon (along with its parents) to the
database.
|
static void |
TaxonSQL.removeGeneticCodeID(java.sql.Connection conn,
DBHelper helper,
Taxon tdb) |
Deprecated.
Deletes the genetic code annotation from the taxon in the database.
|
static void |
TaxonSQL.removeLeftValue(java.sql.Connection conn,
DBHelper helper,
Taxon tdb) |
Deprecated.
Deletes the left value from the specified taxon in the database.
|
static void |
TaxonSQL.removeMitochondrialGeneticCodeID(java.sql.Connection conn,
DBHelper helper,
Taxon tdb) |
Deprecated.
Deletes the so called mitochondrial genetic code annotation from the given taxon.
|
static Taxon |
TaxonSQL.removeName(java.sql.Connection conn,
DBHelper helper,
Taxon taxon,
java.lang.String nameClass,
java.lang.String oldName) |
Deprecated.
Deletes the specified name from of the taxon from the database.
|
static void |
TaxonSQL.removeRank(java.sql.Connection conn,
DBHelper helper,
Taxon tdb) |
Deprecated.
Removes the rank persistently from the taxon in the database.
|
static void |
TaxonSQL.removeRightValue(java.sql.Connection conn,
DBHelper helper,
Taxon tdb) |
Deprecated.
Deletes the right value from the specified taxon in the database.
|
static Taxon |
TaxonSQL.removeTaxon(java.sql.Connection conn,
int ncbi_id,
DBHelper helper) |
Deprecated.
Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the
removed taxon.
|
static Taxon |
TaxonSQL.removeTaxon(java.sql.Connection conn,
DBHelper helper,
java.lang.String name) |
Deprecated.
Deletes a taxon specified by one of it's names with all it's different
names, annotations and sequences from the database.
|