org.biojavax.bio.db.biosql

Class BioSQLFeatureFilter.ContainedByRichLocation

java.lang.Object

org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter

org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation

All Implemented Interfaces:

java.io.Serializable, FeatureFilter, BioSQLFeatureFilter

Enclosing interface:

BioSQLFeatureFilter

public static final class BioSQLFeatureFilter.ContainedByRichLocation
extends BioSQLFeatureFilter.HibernateFeatureFilter

A filter that returns all features contained within a location. Contained means that a feature is entirely within, on the same strand and on the same sequence as 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 and Description
BioSQLFeatureFilter.ContainedByRichLocation(RichLocation loc) Creates a filter that returns everything contained within loc.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(Feature f) Returns true if the feature is within this filter's location.
java.lang.Object	asCriterion() This method returns a Hibernate Criterion object that can be used to query the database.
java.util.Map	criterionAliasMap() Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
boolean	equals(java.lang.Object o)
RichLocation	getRichLocation()
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BioSQLFeatureFilter.ContainedByRichLocation

public BioSQLFeatureFilter.ContainedByRichLocation(RichLocation loc)

Creates a filter that returns everything contained within loc.

Parameters:

loc - the location that will contain the accepted features

Method Detail

getRichLocation

public RichLocation getRichLocation()

accept

public boolean accept(Feature f)

Returns true if the feature is within 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 java.lang.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 java.util.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(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object