- All Known Implementing Classes:
public interface BioSQLFeatureFilter extends FeatureFilterA filter for accepting or rejecting a feature.
It is possible to write custom
FeatureFilters by implementing this interface. There are also a wide range of built-in features, and it is possible to build complex queries using
FeatureFilter.Not. Where possible, use of the built-in filters is preferable to writing new filters, since the methods in the
FilterUtilsclass have access to special knowledge about the built-in filter types and how they relate to one another.
If the filter is to be used in a remote process, it is recognized that it may be serialized and sent over to run remotely, rather than each feature being retrieved locally.
This class requires the Hibernate JAR files to be on your classpath at runtime. It is designed ONLY for use with BioSQLRichSequenceDB and BioSQLBioEntryDB.
- 1.5, 1.5
- Matthew Pocock, Thomas Down, Richard Holland
Nested Class Summary
Nested Classes Modifier and Type Interface Description
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).
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureFilter
FeatureFilter.AnnotationContains, FeatureFilter.ByAncestor, FeatureFilter.ByAnnotation, FeatureFilter.ByAnnotationType, FeatureFilter.ByChild, FeatureFilter.ByClass, FeatureFilter.ByComponentName, FeatureFilter.ByDescendant, FeatureFilter.ByFeature, FeatureFilter.ByPairwiseScore, FeatureFilter.ByParent, FeatureFilter.BySource, FeatureFilter.ByType, FeatureFilter.ContainedByLocation, FeatureFilter.FrameFilter, FeatureFilter.HasAnnotation, FeatureFilter.OnlyChildren, FeatureFilter.OnlyDescendants, FeatureFilter.OverlapsLocation, FeatureFilter.ShadowContainedByLocation, FeatureFilter.ShadowOverlapsLocation, FeatureFilter.StrandFilter
All Methods Instance Methods Abstract Methods Modifier and Type Method Description
asCriterion()This method returns a Hibernate Criterion object that can be used to query the database.
criterionAliasMap()Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
asCriterionThis method returns a Hibernate Criterion object that can be used to query the database.
- a Hibernate Criterion object representing this filter.
criterionAliasMapReturns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all. If not, then it must at least return the empty map else you'll get NullPointerExceptions thrown elsewhere.
- Map a map of property names to aliases used in the criterion.