org.biojavax.bio.db.biosql
Class BioSQLFeatureFilter.OverlapsRichLocation

java.lang.Object
  extended by org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
      extended by org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
All Implemented Interfaces:
java.io.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
BioSQLFeatureFilter.OverlapsRichLocation(RichLocation loc)
          Creates a filter that returns everything overlapping loc.
 
Method Summary
 boolean accept(Feature f)
          Returns true if the feature overlaps 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.OverlapsRichLocation

public BioSQLFeatureFilter.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 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