org.biojava.bio.seq.db.biosql

Class TaxonSQL

java.lang.Object

org.biojava.bio.seq.db.biosql.TaxonSQL

Deprecated.

Use hibernate and org.biojavax.bio.db.*

public class TaxonSQL
extends Object

Methods for retrieving, storing and manipulate Taxa stored in a BioSQL database.

Author:

Len Trigg, Andreas Dräger

Constructor Summary

Constructors

Constructor and Description
TaxonSQL() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
static Taxon	addName(Connection conn, Taxon taxon, String nameClass, String newName) Deprecated. Adds a new name of the given nameClass to the taxon.
static void	attemptClose(ResultSet resultset) Deprecated. Attempt to close the ResultSet.
static void	attemptClose(Statement statement) Deprecated. Attempt to close the Statement.
static void	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.
static String[]	getAllScientificNames(Connection conn) Deprecated. Returns all the scientific names, which are currently stored in the database.
static Stack	getChildrenOf(Connection conn, String scientificName) Deprecated. Returns all children of the specified taxon.
static Stack	getChildrenOf(Connection conn, Taxon t) Deprecated. Returns the children as a Stack of this given taxon.
static Taxon	getDBTaxon(Connection conn, int taxon_id) Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).
static String	getRealScientificName(Taxon t) Deprecated. This returns the true scientific name of a given taxon, if there is one.
static Taxon	getTaxon(Connection conn, int ncbi_taxon_id) Deprecated. Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.
static Taxon	getTaxon(Connection conn, String name) Deprecated. Attempts to get a Taxon object corresponding to the specified name.
static Set	NCBIids(Connection conn) Deprecated. Returns a Set of all NCBI-Taxon-IDs which are currently stored in the database.
static int	putTaxon(Connection conn, DBHelper helper, Taxon taxon) Deprecated. Adds a Taxon (along with its parents) to the database.
static void	removeGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb) Deprecated. Deletes the genetic code annotation from the taxon in the database.
static void	removeLeftValue(Connection conn, DBHelper helper, Taxon tdb) Deprecated. Deletes the left value from the specified taxon in the database.
static void	removeMitochondrialGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb) Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon.
static Taxon	removeName(Connection conn, DBHelper helper, Taxon taxon, String nameClass, String oldName) Deprecated. Deletes the specified name from of the taxon from the database.
static void	removeRank(Connection conn, DBHelper helper, Taxon tdb) Deprecated. Removes the rank persistently from the taxon in the database.
static void	removeRightValue(Connection conn, DBHelper helper, Taxon tdb) Deprecated. Deletes the right value from the specified taxon in the database.
static Taxon	removeTaxon(Connection conn, DBHelper helper, 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	removeTaxon(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	setCommonName(Connection conn, Taxon taxon, 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	setGeneticCodeID(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	setLeftValue(Connection conn, Taxon tdb, int left) Deprecated. Updates the taxon and sets the left value to the specified value.
static void	setMitochondrialGeneticCodeID(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	setParent(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	setRank(Connection conn, Taxon tdb, String rank) Deprecated. Updates a taxon and sets it's rank to the specified String.
static void	setRightValue(Connection conn, Taxon tdb, int right) Deprecated. Updates the taxon in the database and sets the right value to the specified value.
static Taxon	setScientificName(Connection conn, Taxon taxon, String newName) Deprecated. This changes the scientific name of the given taxon and stores the new name persistent in the database.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TaxonSQL

public TaxonSQL()

Deprecated.

Method Detail

getTaxon

public static Taxon getTaxon(Connection conn,
             int ncbi_taxon_id)

Deprecated.

Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.

Parameters:

conn - the connection to the database

ncbi_taxon_id - the NCBI taxon ID.

Returns:

the corresponding Taxon (which may have already been present in memory after an earlier retrieval), or null if the Taxon could not be found in the database.

getDBTaxon

public static Taxon getDBTaxon(Connection conn,
               int taxon_id)
                        throws SQLException,
                               ChangeVetoException

Deprecated.

Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).

Parameters:

conn - the connection to the database

taxon_id - the database-specific id for the Taxon.

Returns:

the corresponding Taxon (which may have already been present in memory after an earlier retrieval).

Throws:

SQLException

ChangeVetoException

putTaxon

public static int putTaxon(Connection conn,
           DBHelper helper,
           Taxon taxon)
                    throws SQLException

Deprecated.

Adds a Taxon (along with its parents) to the database. If it is already present in the database, no action is taken. Returns the id by which the database refers to the specified Taxon object.

Parameters:

taxon - a Taxon. The Taxon must be annotated with the NCBI taxon id (key=EbiFormat.PROPERTY_ORGANISM).

helper - for the certain database system which is in use.

Returns:

an int that corresponds to the Taxon in the database.

Throws:

SQLException

attemptClose

public static void attemptClose(Statement statement)

Deprecated.

Attempt to close the Statement. Continue on if there is a problem during the close.

attemptClose

public static void attemptClose(ResultSet resultset)

Deprecated.

Attempt to close the ResultSet. Continue on if there is a problem during the close.

getTaxon

public static Taxon getTaxon(Connection conn,
             String name)
                      throws BioRuntimeException

Deprecated.

Attempts to get a Taxon object corresponding to the specified name.

Parameters:

conn - the connection to the database

name - the species scientific name

Returns:

the corresponding Taxon (which may have already been present in memory after an earlier retrieval), or null if the Taxon could not be found in the database.

Throws:

BioRuntimeException

getAllScientificNames

public static String[] getAllScientificNames(Connection conn)
                                      throws BioRuntimeException

Deprecated.

Returns all the scientific names, which are currently stored in the database.

Parameters:

conn - connection to the database

Returns:

array of lexicographically sorted Strings

Throws:

BioRuntimeException

getRealScientificName

public static String getRealScientificName(Taxon t)

Deprecated.

This returns the true scientific name of a given taxon, if there is one. This is necessary because if a taxon does not have a parent node, a TaxonFactory gives the scientific name 'ROOT' and the real scientific name (if there is one) is only stored in the taxon's EbiFormat-annotation. This name 'ROOT' applies only for in memory taxon objects. In the database the real name is stored.

Parameters:

t - the taxon

Returns:

Name of the taxon.

NCBIids

public static Set NCBIids(Connection conn)
                   throws BioRuntimeException

Deprecated.

Returns a Set of all NCBI-Taxon-IDs which are currently stored in the database. So it is easy to proove if a taxon is stored in the database or perform other operations.

Parameters:

conn - database connection

Returns:

a Set containing all NCBI-IDs.

Throws:

BioRuntimeException

removeTaxon

public static Taxon removeTaxon(Connection conn,
                DBHelper helper,
                String name)
                         throws SQLException,
                                BioException

Deprecated.

Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database. This cannot be undone. The removed taxon will be returned.

Parameters:

conn - database connection

helper - the helper for the certain database system to be used.

name - one of the taxon's names

Returns:

the taxon, which was successfully removed and which is not longer stored in the database.

Throws:

BioException

SQLException

removeTaxon

public static Taxon removeTaxon(Connection conn,
                int ncbi_id,
                DBHelper helper)
                         throws BioRuntimeException,
                                SQLException,
                                BioException

Deprecated.

Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.

Parameters:

conn - database connection

helper - the helper for the database

ncbi_id - the ncbi-id

Returns:

the taxon wich is not stored in the database anymore.

Throws:

BioRuntimeException

BioException

SQLException

setScientificName

public static Taxon setScientificName(Connection conn,
                      Taxon taxon,
                      String newName)
                               throws SQLException

Deprecated.

This changes the scientific name of the given taxon and stores the new name persistent in the database.

Parameters:

conn - database connection

taxon - the taxon to be changed

newName - the new scientific name

Returns:

the changed taxon with the new scientific name.

Throws:

SQLException

setCommonName

public static Taxon setCommonName(Connection conn,
                  Taxon taxon,
                  String newName)
                           throws BioException,
                                  SQLException

Deprecated.

With this method the common name of the given taxon can be changed or created, if there was none before. The new common name will be stored persitently.

Parameters:

conn - database connection

taxon - the taxon to be updated

newName - the new common name

Returns:

the updated taxon.

Throws:

BioException

SQLException

addName

public static Taxon addName(Connection conn,
            Taxon taxon,
            String nameClass,
            String newName)
                     throws BioException,
                            SQLException,
                            BioRuntimeException

Deprecated.

Adds a new name of the given nameClass to the taxon. However, there must be exactly one scientific name and maximal one common name. Otherwise an Exception will be thrown.

Parameters:

conn - database connection

taxon - the taxon to be updated

nameClass - the name_class of the new name.

newName - the new name.

Returns:

the persistently updated taxon.

Throws:

BioException

SQLException

BioRuntimeException

removeName

public static Taxon removeName(Connection conn,
               DBHelper helper,
               Taxon taxon,
               String nameClass,
               String oldName)
                        throws BioException,
                               SQLException

Deprecated.

Deletes the specified name from of the taxon from the database. The scientific name has to be uniqe, so this cannot be removed by this method.

Parameters:

conn - the database connection

helper - the helper for the used database system

taxon - the taxon to be updated

nameClass - the name_class of the name to be removed

oldName - the old name, which is not needed anymore.

Returns:

the updated taxon.

Throws:

BioException

SQLException

getChildrenOf

public static Stack getChildrenOf(Connection conn,
                  String scientificName)
                           throws BioException

Deprecated.

Returns all children of the specified taxon.

Parameters:

conn - database connection

scientificName - name of the taxon which children should be searched.

Returns:

a Stac, which contains the children sorted by theire scientific names from top to the bottom.

Throws:

BioException

SQLException

getChildrenOf

public static Stack getChildrenOf(Connection conn,
                  Taxon t)
                           throws BioException

Deprecated.

Returns the children as a Stack of this given taxon.

Parameters:

conn - database connection

t - the parent taxon

Returns:

a sorted Stack of the children, which might be empty, but not null.

Throws:

BioException

setRank

public static void setRank(Connection conn,
           Taxon tdb,
           String rank)
                    throws BioRuntimeException

Deprecated.

Updates a taxon and sets it's rank to the specified String.

Parameters:

conn - database connection.

tdb - taxon to be updated

rank - the new rank (like 'kingdom', 'genus' or what ever)

Throws:

BioRuntimeException

removeRank

public static void removeRank(Connection conn,
              DBHelper helper,
              Taxon tdb)
                       throws BioRuntimeException

Deprecated.

Removes the rank persistently from the taxon in the database.

Parameters:

conn -

helper -

tdb -

Throws:

BioRuntimeException

setGeneticCodeID

public static void setGeneticCodeID(Connection conn,
                    Taxon tdb,
                    int id)
                             throws BioRuntimeException

Deprecated.

Updates the taxon in the database and sets its genetic code id to the specified value.

Parameters:

conn -

tdb -

id -

Throws:

BioRuntimeException

removeGeneticCodeID

public static void removeGeneticCodeID(Connection conn,
                       DBHelper helper,
                       Taxon tdb)
                                throws BioRuntimeException

Deprecated.

Deletes the genetic code annotation from the taxon in the database.

Parameters:

conn -

helper -

tdb -

Throws:

BioRuntimeException

setMitochondrialGeneticCodeID

public static void setMitochondrialGeneticCodeID(Connection conn,
                                 Taxon tdb,
                                 int id)
                                          throws BioRuntimeException

Deprecated.

Updates the given taxon and sets it's so called mitochondrial genetic code id to the specified value.

Parameters:

conn -

tdb -

id -

Throws:

BioRuntimeException

removeMitochondrialGeneticCodeID

public static void removeMitochondrialGeneticCodeID(Connection conn,
                                    DBHelper helper,
                                    Taxon tdb)
                                             throws BioRuntimeException

Deprecated.

Deletes the so called mitochondrial genetic code annotation from the given taxon.

Parameters:

conn -

helper -

tdb -

Throws:

BioRuntimeException

setLeftValue

public static void setLeftValue(Connection conn,
                Taxon tdb,
                int left)
                         throws BioRuntimeException

Deprecated.

Updates the taxon and sets the left value to the specified value.

Parameters:

conn -

tdb -

left -

Throws:

BioRuntimeException

removeLeftValue

public static void removeLeftValue(Connection conn,
                   DBHelper helper,
                   Taxon tdb)
                            throws BioRuntimeException

Deprecated.

Deletes the left value from the specified taxon in the database.

Parameters:

conn -

helper -

tdb -

Throws:

BioRuntimeException

setRightValue

public static void setRightValue(Connection conn,
                 Taxon tdb,
                 int right)
                          throws BioRuntimeException

Deprecated.

Updates the taxon in the database and sets the right value to the specified value.

Parameters:

conn -

tdb -

right -

Throws:

BioRuntimeException

removeRightValue

public static void removeRightValue(Connection conn,
                    DBHelper helper,
                    Taxon tdb)
                             throws BioRuntimeException

Deprecated.

Deletes the right value from the specified taxon in the database.

Parameters:

conn -

helper -

tdb -

Throws:

BioRuntimeException

setParent

public static void setParent(Connection conn,
             Taxon child,
             Taxon parent)
                      throws BioRuntimeException

Deprecated.

This updates the taxonomic tree in the database and sets the parent of the given child taxon to the parent taxon.

Parameters:

conn -

child -

parent -

Throws:

BioRuntimeException

automaticUpdate

public static void automaticUpdate(Connection conn,
                   DBHelper helper,
                   TaxonFactory factory,
                   File delnodes,
                   File merged)
                            throws IOException

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.

Parameters:

conn - database connection

helper - helper for the database system to be used

factory - the TaxonFactory containing all the new taxa

delnodes - file containing the ncbi taxon ids which don't exist anymore

merged - file containing the ncbi taxon ids which were merged.

Throws:

IOException