Package | Description |
---|---|
org.biojava.bio.seq.db.biosql |
General purpose Sequence storage in a relational database.
|
org.biojava.bio.taxa |
Taxonomy object for representing species information.
|
Modifier and Type | Method and Description |
---|---|
static Taxon |
TaxonSQL.addName(java.sql.Connection conn,
Taxon taxon,
java.lang.String nameClass,
java.lang.String newName)
Deprecated.
Adds a new name of the given
nameClass to the taxon. |
static Taxon |
TaxonSQL.getDBTaxon(java.sql.Connection conn,
int taxon_id)
Deprecated.
Attempts to get a Taxon object corresponding to the specified
taxon_id (i.e.
|
static Taxon |
TaxonSQL.getTaxon(java.sql.Connection conn,
int ncbi_taxon_id)
Deprecated.
Attempts to get a Taxon object corresponding to the specified
NCBI taxon ID.
|
static Taxon |
TaxonSQL.getTaxon(java.sql.Connection conn,
java.lang.String name)
Deprecated.
Attempts to get a Taxon object corresponding to the specified
name.
|
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 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.
|
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.setCommonName(java.sql.Connection conn,
Taxon taxon,
java.lang.String newName)
Deprecated.
With this method the common name of the given taxon can be changed or created,
if there was none before.
|
static Taxon |
TaxonSQL.setScientificName(java.sql.Connection conn,
Taxon taxon,
java.lang.String newName)
Deprecated.
This changes the scientific name of the given taxon and stores the new name persistent
in the database.
|
Modifier and Type | Method and Description |
---|---|
static Taxon |
TaxonSQL.addName(java.sql.Connection conn,
Taxon taxon,
java.lang.String nameClass,
java.lang.String newName)
Deprecated.
Adds a new name of the given
nameClass to the taxon. |
static java.util.Stack |
TaxonSQL.getChildrenOf(java.sql.Connection conn,
Taxon t)
Deprecated.
Returns the children as a
Stack of this given taxon. |
static java.lang.String |
TaxonSQL.getRealScientificName(Taxon t)
Deprecated.
This returns the true scientific name of a given taxon, if there is one.
|
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.setCommonName(java.sql.Connection conn,
Taxon taxon,
java.lang.String newName)
Deprecated.
With this method the common name of the given taxon can be changed or created,
if there was none before.
|
static void |
TaxonSQL.setGeneticCodeID(java.sql.Connection conn,
Taxon tdb,
int id)
Deprecated.
Updates the taxon in the database and sets its genetic code id to the specified value.
|
static void |
TaxonSQL.setLeftValue(java.sql.Connection conn,
Taxon tdb,
int left)
Deprecated.
Updates the taxon and sets the left value to the specified value.
|
static void |
TaxonSQL.setMitochondrialGeneticCodeID(java.sql.Connection conn,
Taxon tdb,
int id)
Deprecated.
Updates the given taxon and sets it's so called mitochondrial genetic code id to
the specified value.
|
static void |
TaxonSQL.setParent(java.sql.Connection conn,
Taxon child,
Taxon parent)
Deprecated.
This updates the taxonomic tree in the database and sets the parent of the given
child taxon to the parent taxon.
|
static void |
TaxonSQL.setRank(java.sql.Connection conn,
Taxon tdb,
java.lang.String rank)
Deprecated.
Updates a taxon and sets it's rank to the specified
String . |
static void |
TaxonSQL.setRightValue(java.sql.Connection conn,
Taxon tdb,
int right)
Deprecated.
Updates the taxon in the database and sets the right value to the specified value.
|
static Taxon |
TaxonSQL.setScientificName(java.sql.Connection conn,
Taxon taxon,
java.lang.String newName)
Deprecated.
This changes the scientific name of the given taxon and stores the new name persistent
in the database.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractTaxon
Deprecated.
replaced by classes in
org.biojavax.bio.taxa |
class |
SimpleTaxon
Deprecated.
replaced by classes in
org.biojavax.bio.taxa |
class |
WeakTaxon
Deprecated.
replaced by classes in
org.biojavax.bio.taxa |
Modifier and Type | Field and Description |
---|---|
protected Taxon |
SimpleTaxon.parent
Deprecated.
|
protected Taxon |
WeakTaxon.parent
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
Add a taxon as a child to a parent.
|
Taxon |
WeakTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
SimpleTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
TaxonFactory.createTaxon(java.lang.String scientificName,
java.lang.String commonName)
Deprecated.
Create a new orphan Taxon with a given scientific and common
name.
|
Taxon |
WeakTaxonFactory.createTaxon(java.lang.String scientificName,
java.lang.String commonName)
Deprecated.
|
Taxon |
SimpleTaxonFactory.createTaxon(java.lang.String scientificName,
java.lang.String commonName)
Deprecated.
|
Taxon |
SimpleTaxon.getParent()
Deprecated.
|
Taxon |
WeakTaxon.getParent()
Deprecated.
|
Taxon |
Taxon.getParent()
Deprecated.
The parent of this Taxon.
|
Taxon |
TaxonFactory.getRoot()
Deprecated.
Retrieve the root upon which all rooted Taxon that this
factory knows about are rooted.
|
Taxon |
WeakTaxonFactory.getRoot()
Deprecated.
|
Taxon |
SimpleTaxonFactory.getRoot()
Deprecated.
|
Taxon |
TaxonFactory.importTaxon(Taxon source)
Deprecated.
Import a Taxon and all its children into the implementation
provided by this factory.
|
Taxon |
WeakTaxonFactory.importTaxon(Taxon taxon)
Deprecated.
|
Taxon |
SimpleTaxonFactory.importTaxon(Taxon taxon)
Deprecated.
|
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.
|
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
Remove a Taxon as a child to this one.
|
Taxon |
WeakTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
SimpleTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
TaxonFactory.search(java.lang.Object id)
Deprecated.
Retrieve a Taxon that matches some ID.
|
Taxon |
WeakTaxonFactory.search(java.lang.Object id)
Deprecated.
|
Taxon |
SimpleTaxonFactory.search(java.lang.Object id)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
Add a taxon as a child to a parent.
|
Taxon |
WeakTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
SimpleTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
TaxonFactory.importTaxon(Taxon source)
Deprecated.
Import a Taxon and all its children into the implementation
provided by this factory.
|
Taxon |
WeakTaxonFactory.importTaxon(Taxon taxon)
Deprecated.
|
Taxon |
SimpleTaxonFactory.importTaxon(Taxon taxon)
Deprecated.
|
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
Remove a Taxon as a child to this one.
|
Taxon |
WeakTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
|
Taxon |
SimpleTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated.
|
java.lang.String |
TaxonParser.serialize(Taxon taxon)
Deprecated.
Convert a Taxon into a stringified representation.
|
java.lang.String |
EbiFormat.serialize(Taxon taxon)
Deprecated.
|
java.lang.String |
EbiFormat.serializeSource(Taxon taxon)
Deprecated.
|
java.lang.String |
EbiFormat.serializeXRef(Taxon taxon)
Deprecated.
|