Interface BioSQLFeatureFilter
- All Superinterfaces:
FeatureFilter
,Serializable
- All Known Implementing Classes:
BioSQLAcceptAllFilter
,BioSQLAcceptNoneFilter
,BioSQLFeatureFilter.And
,BioSQLFeatureFilter.ByName
,BioSQLFeatureFilter.ByNote
,BioSQLFeatureFilter.ByNoteTermOnly
,BioSQLFeatureFilter.ByRank
,BioSQLFeatureFilter.BySequenceName
,BioSQLFeatureFilter.BySourceTerm
,BioSQLFeatureFilter.BySourceTermName
,BioSQLFeatureFilter.ByStrand
,BioSQLFeatureFilter.ByTypeTerm
,BioSQLFeatureFilter.ByTypeTermName
,BioSQLFeatureFilter.ContainedByRichLocation
,BioSQLFeatureFilter.HibernateFeatureFilter
,BioSQLFeatureFilter.Not
,BioSQLFeatureFilter.Or
,BioSQLFeatureFilter.OverlapsRichLocation
It is possible to write custom FeatureFilter
s by implementing this
interface. There are also a wide range of built-in features, and it is possible
to build complex queries using FeatureFilter.And
, FeatureFilter.Or
,
and FeatureFilter.Not
. Where possible, use of the built-in filters
is preferable to writing new filters, since the methods in the FilterUtils
class 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.
- Since:
- 1.5, 1.5
- Author:
- Matthew Pocock, Thomas Down, Richard Holland
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
A filter that returns all features accepted by both child filter.static final class
Construct one of these to filter features by display name.static final class
A filter that returns all features that have the given note, and the value and rank is checked as well.static final class
A filter that returns all features that have a note with the given term.static final class
Construct one of these to filter features by rank.static final class
Accept features that reside on a sequence with a particular name.static final class
Construct one of these to filter features by source.static final class
Construct one of these to filter features by source (name only - parent ontology is ignored).static final class
A filter that returns all features having locations on a given strand.static final class
Construct one of these to filter features by type.static final class
Construct one of these to filter features by type (name only - parent ontology is ignored).static final class
A filter that returns all features contained within a location.static class
A filter for Hibernate-BioSQL filters to extend.static final class
A filter that returns all features not accepted by a child filter.static final class
A filter that returns all features accepted by at least one child filter.static final class
A filter that returns all features overlapping a location.static class
A 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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final BioSQLFeatureFilter
All features are selected by this filter.static final BioSQLFeatureFilter
No features are selected by this filter.Fields inherited from interface org.biojava.bio.seq.FeatureFilter
leaf, top_level
-
Method Summary
Modifier and TypeMethodDescriptionThis method returns a Hibernate Criterion object that can be used to query the database.Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.Methods inherited from interface org.biojava.bio.seq.FeatureFilter
accept
-
Field Details
-
all
All features are selected by this filter. -
none
No features are selected by this filter.
-
-
Method Details
-
asCriterion
This method returns a Hibernate Criterion object that can be used to query the database.- Returns:
- a Hibernate Criterion object representing this filter.
-
criterionAliasMap
Returns 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.- Returns:
- Map a map of property names to aliases used in the criterion.
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