AnnotationDB (biojava-legacy 1.9.1 API)

All Known Implementing Classes:

IndexedAnnotationDB, LazyFilteredAnnotationDB, LazySearchedAnnotationDB, MergingAnnotationDB, SimpleAnnotationDB
```
public interface AnnotationDB
```
A database of Annotation instances.

It is often a pain to provide explicit API for a particular file format, but it is still necisary to present it as some collection of structured objects. Annotation, together with AnnotationType are capable of representing structured data and the tag-value parser API is uniquely suited to creating these from structured text files. AnnotationDB is provided as a way to wrap up a whole collection of Annotation instances so that they can be queried and handled as a unit.

Since:

1.3

Author:

Matthew Pocock

Field Summary

Fields
Modifier and Type Field and Description

static AnnotationDB EMPTY
An AnnotationDB that is always empty.

Fields
Modifier and Type	Field and Description
`static AnnotationDB`	`EMPTY` An AnnotationDB that is always empty.

Method Summary

Methods
Modifier and Type	Method and Description
`AnnotationDB`	`filter(AnnotationType at)` Find all Annotation instances in this DB that are of a particular type.
`String`	`getName()` The name of this AnnotationDB.
`AnnotationType`	`getSchema()` Get an AnnotationType that accepts all Annotation instances in this DB.
`Iterator`	`iterator()` Loop over each Annotation in this db.
`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.

- Field Detail
  - EMPTY
```
static final AnnotationDB EMPTY
```
    An AnnotationDB that is always empty.
- Method Detail
  - getName
```
String getName()
```
    The name of this AnnotationDB.
    
    Returns:
    the name of this AnnotationDB
  - getSchema
```
AnnotationType getSchema()
```
    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.
    
    Returns:
    the schema AnnotationType
  - iterator
```
Iterator iterator()
```
    Loop over each Annotation in this db.
    
    Returns:
    an Iterator over each item in the DB
  - size
```
int size()
```
    The number of Annotation instances in the DB.
    
    Returns:
    the size of this DB
  - filter
```
AnnotationDB filter(AnnotationType at)
```
    Find all Annotation instances in this DB that are of a particular type.
    
    Parameters:
    at - the AnnotationType to match
    
    Returns:
    an AnnotationDB with all matching Annotation instances
  - search
```
AnnotationDB search(AnnotationType at)
```
    Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.
    
    Parameters:
    at - the AnnotationType to search with
    
    Returns:
    an AnnotationDB with all matching Annotation instances, irregardless of how deep in the hieracy they are

Interface AnnotationDB

Field Summary

Method Summary

Field Detail

EMPTY

Method Detail

getName

getSchema

iterator

size

filter

search