org.biojavax.bio.db.biosql

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

public interface BioSQLFeatureFilter
extends FeatureFilter

A 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.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 Classes

Modifier and Type	Interface and Description
static class	BioSQLFeatureFilter.And A filter that returns all features accepted by both child filter.
static class	BioSQLFeatureFilter.ByName Construct one of these to filter features by display name.
static class	BioSQLFeatureFilter.ByNote A filter that returns all features that have the given note, and the value and rank is checked as well.
static class	BioSQLFeatureFilter.ByNoteTermOnly A filter that returns all features that have a note with the given term.
static class	BioSQLFeatureFilter.ByRank Construct one of these to filter features by rank.
static class	BioSQLFeatureFilter.BySequenceName Accept features that reside on a sequence with a particular name.
static class	BioSQLFeatureFilter.BySourceTerm Construct one of these to filter features by source.
static class	BioSQLFeatureFilter.BySourceTermName Construct one of these to filter features by source (name only - parent ontology is ignored).
static class	BioSQLFeatureFilter.ByStrand A filter that returns all features having locations on a given strand.
static class	BioSQLFeatureFilter.ByTypeTerm Construct one of these to filter features by type.
static class	BioSQLFeatureFilter.ByTypeTermName Construct one of these to filter features by type (name only - parent ontology is ignored).
static class	BioSQLFeatureFilter.ContainedByRichLocation A filter that returns all features contained within a location.
static class	BioSQLFeatureFilter.HibernateFeatureFilter A filter for Hibernate-BioSQL filters to extend.
static class	BioSQLFeatureFilter.Not A filter that returns all features not accepted by a child filter.
static class	BioSQLFeatureFilter.Or A filter that returns all features accepted by at least one child filter.
static class	BioSQLFeatureFilter.OverlapsRichLocation A filter that returns all features overlapping a location.
static class	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).

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

Field Summary

Fields

Modifier and Type	Field and Description
static BioSQLFeatureFilter	all All features are selected by this filter.
static BioSQLFeatureFilter	none No features are selected by this filter.

Fields inherited from interface org.biojava.bio.seq.FeatureFilter

leaf, top_level

Method Summary

Modifier and Type	Method and Description
Object	asCriterion() This method returns a Hibernate Criterion object that can be used to query the database.
Map	criterionAliasMap() 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 Detail

all

static final BioSQLFeatureFilter all

All features are selected by this filter.

none

static final BioSQLFeatureFilter none

No features are selected by this filter.

Method Detail

asCriterion

Object 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

Map 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.