## Uses of Class
org.biojava.bio.BioRuntimeException

Packages that use BioRuntimeException
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
org.biojava.bio.seq.db: Collections of biological sequence data.
org.biojava.bio.seq.db.biosql: General purpose Sequence storage in a relational database.

Uses of BioRuntimeException in org.biojava.bio.alignment

Subclasses of BioRuntimeException in org.biojava.bio.alignment
`class` `IllegalAlignmentEditException` The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.

Methods in org.biojava.bio.alignment that throw BioRuntimeException
`double` `SmithWaterman.pairwiseAlignment(Sequence query, Sequence subject)` Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
`double` `NeedlemanWunsch.pairwiseAlignment(Sequence query, Sequence subject)` Global pairwise sequence alginment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.

Uses of BioRuntimeException in org.biojava.bio.seq.db

Constructors in org.biojava.bio.seq.db that throw BioRuntimeException
`NCBISequenceDB(java.lang.String server, java.lang.String CGI, java.lang.String database, SequenceFormat format)` Parameterized constructor

Uses of BioRuntimeException in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that throw BioRuntimeException
`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.lang.String[]` `TaxonSQL.getAllScientificNames(java.sql.Connection conn)` Deprecated. Returns all the `scientific name`s, which are currently stored in the database.
`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 java.util.Set` `TaxonSQL.NCBIids(java.sql.Connection conn)` Deprecated. Returns a `Set` of all NCBI-Taxon-IDs which are currently stored in 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 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.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 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.