Uses of Class
org.biojava.bio.BioRuntimeException
Packages that use BioRuntimeException
Package
Description
Classes to generate and describe sequence alignments.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
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Uses of BioRuntimeException in org.biojava.bio.alignment
Subclasses of BioRuntimeException in org.biojava.bio.alignmentModifier and TypeClassDescriptionclass
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 BioRuntimeExceptionModifier and TypeMethodDescriptionSmithWaterman.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 BioRuntimeExceptionModifierConstructorDescriptionNCBISequenceDB
(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 BioRuntimeExceptionModifier and TypeMethodDescriptionstatic Taxon
TaxonSQL.addName
(Connection conn, Taxon taxon, String nameClass, String newName) Deprecated.Adds a new name of the givennameClass
to the taxon.static String[]
TaxonSQL.getAllScientificNames
(Connection conn) Deprecated.Returns all thescientific 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 aSet
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 specifiedString
.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.