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

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()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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 interface BioSQLFeatureFilter

Overrides:

criterionAliasMap in class BioSQLFeatureFilter.HibernateFeatureFilter

Returns:

Map a map of property names to aliases used in the criterion.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object