Class MergingAnnotationDB

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

public class MergingAnnotationDB extends Object implements AnnotationDB

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

Since:
1.3
Author:
Matthew Pocock
  • Constructor Details

    • MergingAnnotationDB

      Create a new MergingAnnotationDB with a name and no DBs to merge.
      Parameters:
      name - the name of this DB
    • MergingAnnotationDB

      public MergingAnnotationDB(String name, 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 Details

    • 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 List getMerged()
      Return a list of merged DBs. This can be modified independantly of this DB.
      Returns:
      a List of merged DBs
    • getName

      public 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

      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 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

      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

      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