Package org.biojavax.bio.db.biosql

Interface between biojava and biosql databases

Interface Summary

Interface	Description
BioSQLFeatureFilter	A filter for accepting or rejecting a feature.

Class Summary

Class	Description
BioSQLAcceptAllFilter	The class that accepts all features.
BioSQLAcceptNoneFilter	The class that accepts no features.
BioSQLBioEntryDB
BioSQLCrossReferenceResolver	A simple implementation of CrossReferenceResolver
BioSQLFeatureFilter.And	A filter that returns all features accepted by both child filter.
BioSQLFeatureFilter.ByName	Construct one of these to filter features by display name.
BioSQLFeatureFilter.ByNote	A filter that returns all features that have the given note, and the value and rank is checked as well.
BioSQLFeatureFilter.ByNoteTermOnly	A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByRank	Construct one of these to filter features by rank.
BioSQLFeatureFilter.BySequenceName	Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySourceTerm	Construct one of these to filter features by source.
BioSQLFeatureFilter.BySourceTermName	Construct one of these to filter features by source (name only - parent ontology is ignored).
BioSQLFeatureFilter.ByStrand	A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByTypeTerm	Construct one of these to filter features by type.
BioSQLFeatureFilter.ByTypeTermName	Construct one of these to filter features by type (name only - parent ontology is ignored).
BioSQLFeatureFilter.ContainedByRichLocation	A filter that returns all features contained within a location.
BioSQLFeatureFilter.HibernateFeatureFilter	A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.Not	A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Or	A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.OverlapsRichLocation	A filter that returns all features overlapping a location.
BioSQLFeatureFilter.Tools	A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
BioSQLRichObjectBuilder	Takes requests for RichObjects and sees if it can load them from a Hibernate database.
BioSQLRichSequenceDB
BioSQLRichSequenceHandler	A handler which loads sequence data from a BioSQL database, caching it where possible.