Package org.biojava.bio.annodb
Class MergingAnnotationDB
java.lang.Object
org.biojava.bio.annodb.MergingAnnotationDB
- All Implemented Interfaces:
AnnotationDB
An AnnotationDB that provides a merged view of a list of underlying DBs.
- Since:
- 1.3
- Author:
- Matthew Pocock
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Field Summary
Fields inherited from interface org.biojava.bio.annodb.AnnotationDB
EMPTY
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Constructor Summary
ConstructorsConstructorDescriptionMergingAnnotationDB
(String name) Create a new MergingAnnotationDB with a name and no DBs to merge.MergingAnnotationDB
(String name, List merged) Create a new MergingAnnotationDB with a name and a list of DBs to merge. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAnnotationDB
(AnnotationDB toAdd) Add a DB to be merged in this view.filter
(AnnotationType at) Find all Annotation instances in this DB that are of a particular type.Return a list of merged DBs.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.void
removeAnnotationDB
(AnnotationDB toRemove) Remove a DB from this view.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.
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Constructor Details
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MergingAnnotationDB
Create a new MergingAnnotationDB with a name and no DBs to merge.- Parameters:
name
- the name of this DB
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MergingAnnotationDB
Create a new MergingAnnotationDB with a name and a list of DBs to merge.- Parameters:
name
- the name of this DBmerged
- a list of DBs to merge
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Method Details
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addAnnotationDB
Add a DB to be merged in this view.- Parameters:
toAdd
- the AnnotationDB to add
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removeAnnotationDB
Remove a DB from this view.- Parameters:
toRemove
- the AnnotationDB to remove
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getMerged
Return a list of merged DBs. This can be modified independantly of this DB.- Returns:
- a List of merged DBs
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getName
Description copied from interface:AnnotationDB
The name of this AnnotationDB.
- Specified by:
getName
in interfaceAnnotationDB
- Returns:
- the name of this AnnotationDB
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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
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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
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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
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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
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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
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