Package org.biojavax.bio.db.biosql
Class BioSQLFeatureFilter.OverlapsRichLocation
- java.lang.Object
-
- org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
- All Implemented Interfaces:
Serializable
,FeatureFilter
,BioSQLFeatureFilter
- Enclosing interface:
- BioSQLFeatureFilter
public static final class BioSQLFeatureFilter.OverlapsRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter
A filter that returns all features overlapping a location. Overlaps means that a feature includes part of, on the same strand and on the same sequence any single member of the flattened query location.- Since:
- 1.5
- Author:
- Matthew Pocock, Richard Holland
- See Also:
- Serialized Form
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
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, BioSQLFeatureFilter.Tools
-
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 inherited from class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
and, conjunctAdd, conjunction, disjunctAdd, disjunction, eq, ge, le, not, or
-
Fields inherited from interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
all, none
-
Fields inherited from interface org.biojava.bio.seq.FeatureFilter
leaf, top_level
-
-
Constructor Summary
Constructors Constructor Description OverlapsRichLocation(RichLocation loc)
Creates a filter that returns everything overlapping loc.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accept(Feature f)
Returns true if the feature overlaps this filter's location.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.boolean
equals(Object o)
RichLocation
getRichLocation()
int
hashCode()
String
toString()
-
-
-
Constructor Detail
-
OverlapsRichLocation
public OverlapsRichLocation(RichLocation loc)
Creates a filter that returns everything overlapping loc.- Parameters:
loc
- the location that will overlap the accepted features
-
-
Method Detail
-
getRichLocation
public RichLocation getRichLocation()
-
accept
public boolean accept(Feature f)
Returns true if the feature overlaps this filter's location.- Parameters:
f
- the Feature to evaluate- Returns:
- true if this feature is to be selected in, or false if it is to be ignored
-
asCriterion
public Object asCriterion()
Description copied from interface:BioSQLFeatureFilter
This method returns a Hibernate Criterion object that can be used to query the database.- Returns:
- a Hibernate Criterion object representing this filter.
-
criterionAliasMap
public Map criterionAliasMap()
Description copied from interface:BioSQLFeatureFilter
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.- Specified by:
criterionAliasMap
in interfaceBioSQLFeatureFilter
- Overrides:
criterionAliasMap
in classBioSQLFeatureFilter.HibernateFeatureFilter
- Returns:
- Map a map of property names to aliases used in the criterion.
-
-