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

java.lang.Object
  extended by 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
TaxonSQL()
          Deprecated.  
 
Method Summary
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.
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