## 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
`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 name`s, 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 name`s, which are currently stored in the database.

  Parameters:
    `conn` - connection to the database
  Returns:
    array of lexicographically sorted `String`s
  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 name`s 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`