org.biojava.bio.annodb
Class MergingAnnotationDB

java.lang.Object
  extended by org.biojava.bio.annodb.MergingAnnotationDB
All Implemented Interfaces:
AnnotationDB

public class MergingAnnotationDB
extends java.lang.Object
implements AnnotationDB

An AnnotationDB that provides a merged view of a list of underlying DBs.

Since:
1.3
Author:
Matthew Pocock

Field Summary
 
Fields inherited from interface org.biojava.bio.annodb.AnnotationDB
EMPTY
 
Constructor Summary
MergingAnnotationDB(java.lang.String name)
          Create a new MergingAnnotationDB with a name and no DBs to merge.
MergingAnnotationDB(java.lang.String name, java.util.List merged)
          Create a new MergingAnnotationDB with a name and a list of DBs to merge.
 
Method Summary
 void addAnnotationDB(AnnotationDB toAdd)
          Add a DB to be merged in this view.
 AnnotationDB filter(AnnotationType at)
          Find all Annotation instances in this DB that are of a particular type.
 java.util.List getMerged()
          Return a list of merged DBs.
 java.lang.String getName()
          The name of this AnnotationDB.
 AnnotationType getSchema()
           Get an AnnotationType that accepts all Annotation instances in this DB.
 java.util.Iterator iterator()
          Loop over each Annotation in this db.
 void removeAnnotationDB(AnnotationDB toRemove)
          Remove a DB from this view.
 AnnotationDB 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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MergingAnnotationDB

public MergingAnnotationDB(java.lang.String name)
Create a new MergingAnnotationDB with a name and no DBs to merge.

Parameters:
name - the name of this DB

MergingAnnotationDB

public MergingAnnotationDB(java.lang.String name,
                           java.util.List merged)
Create a new MergingAnnotationDB with a name and a list of DBs to merge.

Parameters:
name - the name of this DB
merged - a list of DBs to merge
Method Detail

addAnnotationDB

public void addAnnotationDB(AnnotationDB toAdd)
Add a DB to be merged in this view.

Parameters:
toAdd - the AnnotationDB to add

removeAnnotationDB

public void removeAnnotationDB(AnnotationDB toRemove)
Remove a DB from this view.

Parameters:
toRemove - the AnnotationDB to remove

getMerged

public java.util.List getMerged()
Return a list of merged DBs. This can be modified independantly of this DB.

Returns:
a List of merged DBs

getName

public java.lang.String getName()
Description copied from interface: AnnotationDB

The name of this AnnotationDB.

Specified by:
getName in interface AnnotationDB
Returns:
the name of this AnnotationDB

getSchema

public AnnotationType 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 interface AnnotationDB
Returns:
the schema AnnotationType

iterator

public java.util.Iterator iterator()
Description copied from interface: AnnotationDB
Loop over each Annotation in this db.

Specified by:
iterator in interface AnnotationDB
Returns:
an Iterator over each item in the DB

size

public int size()
Description copied from interface: AnnotationDB
The number of Annotation instances in the DB.

Specified by:
size in interface AnnotationDB
Returns:
the size of this DB

filter

public AnnotationDB filter(AnnotationType at)
Description copied from interface: AnnotationDB
Find all Annotation instances in this DB that are of a particular type.

Specified by:
filter in interface AnnotationDB
Parameters:
at - the AnnotationType to match
Returns:
an AnnotationDB with all matching Annotation instances

search

public AnnotationDB search(AnnotationType at)
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 interface AnnotationDB
Parameters:
at - the AnnotationType to search with
Returns:
an AnnotationDB with all matching Annotation instances, irregardless of how deep in the hieracy they are