Interface between biojava and biosql databases
Interface Summary Interface Description BioSQLFeatureFilterA filter for accepting or rejecting a feature.
Class Summary Class Description BioSQLAcceptAllFilterThe class that accepts all features. BioSQLAcceptNoneFilterThe class that accepts no features. BioSQLBioEntryDB BioSQLCrossReferenceResolverA simple implementation of CrossReferenceResolver BioSQLFeatureFilter.AndA filter that returns all features accepted by both child filter. BioSQLFeatureFilter.ByNameConstruct one of these to filter features by display name. BioSQLFeatureFilter.ByNoteA filter that returns all features that have the given note, and the value and rank is checked as well. BioSQLFeatureFilter.ByNoteTermOnlyA filter that returns all features that have a note with the given term. BioSQLFeatureFilter.ByRankConstruct one of these to filter features by rank. BioSQLFeatureFilter.BySequenceNameAccept features that reside on a sequence with a particular name. BioSQLFeatureFilter.BySourceTermConstruct one of these to filter features by source. BioSQLFeatureFilter.BySourceTermNameConstruct one of these to filter features by source (name only - parent ontology is ignored). BioSQLFeatureFilter.ByStrandA filter that returns all features having locations on a given strand. BioSQLFeatureFilter.ByTypeTermConstruct one of these to filter features by type. BioSQLFeatureFilter.ByTypeTermNameConstruct one of these to filter features by type (name only - parent ontology is ignored). BioSQLFeatureFilter.ContainedByRichLocationA filter that returns all features contained within a location. BioSQLFeatureFilter.HibernateFeatureFilterA filter for Hibernate-BioSQL filters to extend. BioSQLFeatureFilter.NotA filter that returns all features not accepted by a child filter. BioSQLFeatureFilter.OrA filter that returns all features accepted by at least one child filter. BioSQLFeatureFilter.OverlapsRichLocationA filter that returns all features overlapping a location. BioSQLFeatureFilter.ToolsA class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible). BioSQLRichObjectBuilderTakes requests for RichObjects and sees if it can load them from a Hibernate database. BioSQLRichSequenceDB BioSQLRichSequenceHandlerA handler which loads sequence data from a BioSQL database, caching it where possible.