## 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
`int` `SmithWaterman.pairwiseAlignment(SymbolList query, SymbolList subject)` Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
`int` `NeedlemanWunsch.pairwiseAlignment(SymbolList query, SymbolList subject)` Global pairwise sequence alignment 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(String server, String CGI, 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(Connection conn, Taxon taxon, String nameClass, String newName)` Deprecated. Adds a new name of the given `nameClass` to the taxon.
`static String[]` `TaxonSQL.getAllScientificNames(Connection conn)` Deprecated. Returns all the `scientific name`s, which are currently stored in the database.
`static Taxon` `TaxonSQL.getTaxon(Connection conn, String name)` Deprecated. Attempts to get a Taxon object corresponding to the specified name.
`static Set` `TaxonSQL.NCBIids(Connection conn)` Deprecated. Returns a `Set` of all NCBI-Taxon-IDs which are currently stored in the database.
`static void` `TaxonSQL.removeGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb)` Deprecated. Deletes the genetic code annotation from the taxon in the database.
`static void` `TaxonSQL.removeLeftValue(Connection conn, DBHelper helper, Taxon tdb)` Deprecated. Deletes the left value from the specified taxon in the database.
`static void` `TaxonSQL.removeMitochondrialGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb)` Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon.
`static void` `TaxonSQL.removeRank(Connection conn, DBHelper helper, Taxon tdb)` Deprecated. Removes the rank persistently from the taxon in the database.
`static void` `TaxonSQL.removeRightValue(Connection conn, DBHelper helper, Taxon tdb)` Deprecated. Deletes the right value from the specified taxon in the database.
`static Taxon` `TaxonSQL.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 void` `TaxonSQL.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` `TaxonSQL.setLeftValue(Connection conn, Taxon tdb, int left)` Deprecated. Updates the taxon and sets the left value to the specified value.
`static void` `TaxonSQL.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` `TaxonSQL.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` `TaxonSQL.setRank(Connection conn, Taxon tdb, String rank)` Deprecated. Updates a taxon and sets it's rank to the specified `String`.
`static void` `TaxonSQL.setRightValue(Connection conn, Taxon tdb, int right)` Deprecated. Updates the taxon in the database and sets the right value to the specified value.