Class IndexedAnnotationDB

  • All Implemented Interfaces:
    AnnotationDB

    public class IndexedAnnotationDB
    extends java.lang.Object
    implements AnnotationDB

    A database of Annotation instances backed by an indexed file set.

    Since:
    1.3
    Author:
    Matthew Pocock
    • Constructor Detail

      • IndexedAnnotationDB

        public IndexedAnnotationDB​(BioStore store)
                            throws java.io.IOException,
                                   org.xml.sax.SAXException
        Initialise the db from a store.
        Parameters:
        store - the BioStore to initalise from
        Throws:
        java.io.IOException - if there was an IO fault accessing the store
        org.xml.sax.SAXException - if the XML configuration file is corrupted
    • Method Detail

      • 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