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Packages that use Taxon | |
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org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
Uses of Taxon in org.biojava.bio.seq.db.biosql |
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Methods in org.biojava.bio.seq.db.biosql that return Taxon | |
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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. |
Methods in org.biojava.bio.seq.db.biosql with parameters of type Taxon | |
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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. |
Uses of Taxon in org.biojava.bio.taxa |
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Classes in org.biojava.bio.taxa that implement Taxon | |
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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 |
Fields in org.biojava.bio.taxa declared as Taxon | |
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protected Taxon |
SimpleTaxon.parent
Deprecated. |
protected Taxon |
WeakTaxon.parent
Deprecated. |
Methods in org.biojava.bio.taxa that return Taxon | |
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Taxon |
WeakTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. Add a taxon as a child to a parent. |
Taxon |
SimpleTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
WeakTaxonFactory.createTaxon(java.lang.String scientificName,
java.lang.String commonName)
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 |
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 |
WeakTaxonFactory.getRoot()
Deprecated. |
Taxon |
TaxonFactory.getRoot()
Deprecated. Retrieve the root upon which all rooted Taxon that this factory knows about are rooted. |
Taxon |
SimpleTaxonFactory.getRoot()
Deprecated. |
Taxon |
WeakTaxonFactory.importTaxon(Taxon taxon)
Deprecated. |
Taxon |
TaxonFactory.importTaxon(Taxon source)
Deprecated. Import a Taxon and all its children into the implementation provided by this factory. |
Taxon |
SimpleTaxonFactory.importTaxon(Taxon taxon)
Deprecated. |
Taxon |
EbiFormat.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
Deprecated. |
Taxon |
TaxonParser.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
Deprecated. Convert a stringified Taxon into a Taxon instance. |
Taxon |
WeakTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. Remove a Taxon as a child to this one. |
Taxon |
SimpleTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
WeakTaxonFactory.search(java.lang.Object id)
Deprecated. |
Taxon |
TaxonFactory.search(java.lang.Object id)
Deprecated. Retrieve a Taxon that matches some ID. |
Taxon |
SimpleTaxonFactory.search(java.lang.Object id)
Deprecated. |
Methods in org.biojava.bio.taxa with parameters of type Taxon | |
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Taxon |
WeakTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. Add a taxon as a child to a parent. |
Taxon |
SimpleTaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
WeakTaxonFactory.importTaxon(Taxon taxon)
Deprecated. |
Taxon |
TaxonFactory.importTaxon(Taxon source)
Deprecated. Import a Taxon and all its children into the implementation provided by this factory. |
Taxon |
SimpleTaxonFactory.importTaxon(Taxon taxon)
Deprecated. |
Taxon |
WeakTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. |
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. Remove a Taxon as a child to this one. |
Taxon |
SimpleTaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. |
java.lang.String |
EbiFormat.serialize(Taxon taxon)
Deprecated. |
java.lang.String |
TaxonParser.serialize(Taxon taxon)
Deprecated. Convert a Taxon into a stringified representation. |
java.lang.String |
EbiFormat.serializeSource(Taxon taxon)
Deprecated. |
java.lang.String |
EbiFormat.serializeXRef(Taxon taxon)
Deprecated. |
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