Package org.biojava.bio.annodb
Class SimpleAnnotationDB
java.lang.Object
org.biojava.bio.annodb.SimpleAnnotationDB
- All Implemented Interfaces:
AnnotationDB
A no-frills implementation of AnnotationDB.
- Since:
- 1.3
- Author:
- Matthew Pocock
-
Field Summary
Fields inherited from interface org.biojava.bio.annodb.AnnotationDB
EMPTY
-
Constructor Summary
ConstructorsConstructorDescriptionSimpleAnnotationDB
(String name, Set anns, AnnotationType schema) Create a no-frills AnnotationDB instancec. -
Method Summary
Modifier and TypeMethodDescriptionfilter
(AnnotationType at) Find all Annotation instances in this DB that are of a particular type.getName()
The name of this AnnotationDB.Get an AnnotationType that accepts all Annotation instances in this DB.iterator()
Loop over each Annotation in this db.search
(AnnotationType at) Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.int
size()
The number of Annotation instances in the DB.
-
Constructor Details
-
SimpleAnnotationDB
Create a no-frills AnnotationDB instancec.- Parameters:
name
- the name of this Annotation DBanns
- a Set of Annotation instances it containsschema
- an AnnotationType schema that applies to them
-
-
Method Details
-
getName
Description copied from interface:AnnotationDB
The name of this AnnotationDB.
- Specified by:
getName
in interfaceAnnotationDB
- Returns:
- the name of this AnnotationDB
-
size
Description copied from interface:AnnotationDB
The number of Annotation instances in the DB.- Specified by:
size
in interfaceAnnotationDB
- Returns:
- the size of this DB
-
getSchema
Description copied from interface:AnnotationDB
Get an AnnotationType that accepts all Annotation instances in this DB.
The schema should accept all Annotations in the DB. However, it may hit other Annotations. So, AnnotationType.ALL is always a valid schema. Obviously, the more retrictive it is, the more usefull it becomes for introspection.
- Specified by:
getSchema
in interfaceAnnotationDB
- Returns:
- the schema AnnotationType
-
iterator
Description copied from interface:AnnotationDB
Loop over each Annotation in this db.- Specified by:
iterator
in interfaceAnnotationDB
- Returns:
- an Iterator over each item in the DB
-
filter
Description copied from interface:AnnotationDB
Find all Annotation instances in this DB that are of a particular type.- Specified by:
filter
in interfaceAnnotationDB
- Parameters:
at
- the AnnotationType to match- Returns:
- an AnnotationDB with all matching Annotation instances
-
search
Description copied from interface:AnnotationDB
Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.- Specified by:
search
in interfaceAnnotationDB
- Parameters:
at
- the AnnotationType to search with- Returns:
- an AnnotationDB with all matching Annotation instances, irregardless of how deep in the hieracy they are
-