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public interface BioSQLFeatureFilter
A filter for accepting or rejecting a feature.
It is possible to write custom FeatureFilter
s 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.
Nested Class Summary | |
---|---|
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). |
Field Summary | |
---|---|
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 | |
---|---|
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. |
Methods inherited from interface org.biojava.bio.seq.FeatureFilter |
---|
accept |
Field Detail |
---|
static final BioSQLFeatureFilter all
static final BioSQLFeatureFilter none
Method Detail |
---|
java.lang.Object asCriterion()
java.util.Map criterionAliasMap()
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