Uses of Class
org.biojava.bio.BioRuntimeException

Packages that use BioRuntimeException

Package	Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Method and Description
AlignmentPair	SmithWaterman.pairwiseAlignment(SymbolList query, SymbolList subject) Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.

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

Constructors in org.biojava.bio.seq.db that throw BioRuntimeException

Constructor and Description
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

Modifier and Type	Method and Description
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 names, 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.