MergingAnnotationDB (biojava-legacy 1.9.5 API)

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

Field Summary
- Fields inherited from interface org.biojava.bio.annodb.AnnotationDB
  EMPTY

Constructor Summary

Constructors
Constructor	Description
`MergingAnnotationDB(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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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.
`List`	`getMerged()`	Return a list of merged DBs.
`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.
`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(String name)
```
    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 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 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()
```
    The name of this AnnotationDB.
    
    Specified by:
    
    getName in interface AnnotationDB
    
    Returns:
    
    the name of this AnnotationDB
  - getSchema
```
public 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.
    
    Specified by:
    
    getSchema in interface AnnotationDB
    
    Returns:
    
    the schema AnnotationType
  - iterator
```
public Iterator iterator()
```
    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()
```
    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)
```
    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)
```
    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

Field Summary

Fields inherited from interface org.biojava.bio.annodb.AnnotationDB

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MergingAnnotationDB

MergingAnnotationDB

Method Detail

addAnnotationDB

removeAnnotationDB

getMerged

getName

getSchema

iterator

size

filter

search