Package org.biojava.bio.seq

Class FeatureTypes

java.lang.Object

org.biojava.bio.seq.FeatureTypes

public class FeatureTypes
extends Object

Registry of known types of features.

Historically, the type of a feature within a sequence has been represented by the class or interface of the feature, or by the type property. Different databases use different names for types, and the same name can mean different things depending on where it came from.

This class attempts to provide a framework for registering and managing feature types. It includes the concept of a type having a FeatureFilter schema that would match all examples of that type, and a URI for that type. Groups of related types, such as all those defined in embl, can be packaged up into a single namespace. One type can refer to any number of others, indicating that they are direct parents. This lets us say things like an Ensembl exon is a specific type of the general exon type, and also an instance of the Ensembl feature type.

All feature types are presumed to have URIs that are of the form: uri:biojava.org:types:${repository}/${type} where ${repository} is something like embl or ensembl. Feature types defined within biojava will be in the repository called "core". ${type} is the local type of the feature. This will be something like exon, or repeat. The total URI must be unique. Different repositories can (and are encouraged to) define types with the same names.

Since:

1.3

Author:

Matthew Pocock

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	FeatureTypes.Repository	A named collection of Types.
static class	FeatureTypes.RepositoryImpl	A simple implementation of a Repository.
static interface	FeatureTypes.Type	A type of feature.

Field Summary

Fields

Modifier and Type	Field	Description
static String	URI_PREFIX	The standard prefix for all type URIs

Constructor Summary

Constructors

Constructor	Description
FeatureTypes()

Method Summary

Modifier and Type	Method	Description
static void	addRepository(FeatureTypes.Repository repos)	Add a repository to FeatureTypes.
static FeatureTypes.Repository	getRepository(String name)	Fetch a repository by name.
static Set	getRepositoryNames()	Find the names of all known repositories.
static FeatureTypes.Type	getType(String uri)	Get a Type by URI.
static boolean	isSubTypeOf(FeatureTypes.Type subType, FeatureTypes.Type superType)	Work out if one type is a sub-type of another.
static void	removeRepository(FeatureTypes.Repository repos)	Remove a repository from FeaturTypes.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

URI_PREFIX

public static final String URI_PREFIX

The standard prefix for all type URIs

See Also:

Constant Field Values

Constructor Detail

FeatureTypes

public FeatureTypes()

Method Detail

getRepository

public static FeatureTypes.Repository getRepository(String name)
                                             throws NoSuchElementException

Fetch a repository by name.

Use this to find out what types a repository can provide.

Parameters:

name - the name of the Repository to fetch

Returns:

the Repository with that name

Throws:

NoSuchElementException - if there is no repository by that name

getRepositoryNames

public static Set getRepositoryNames()

Find the names of all known repositories.

Returns:

a Set of all repository names

addRepository

public static void addRepository(FeatureTypes.Repository repos)

Add a repository to FeatureTypes.

Parameters:

repos - the Repository to add

removeRepository

public static void removeRepository(FeatureTypes.Repository repos)

Remove a repository from FeaturTypes.

Parameters:

repos - the Repository to remove

getType

public static FeatureTypes.Type getType(String uri)

Get a Type by URI.

This will attemt to resolve the URI to a type by first matching the standard prefix, then finding a repository of the right name and finally searching that with the type-name portion of the URI.

Parameters:

uri - the URI to resolve

Returns:

a Type with that URI

Throws:

NoSuchElementException - if the type could not be resolved

isSubTypeOf

public static boolean isSubTypeOf(FeatureTypes.Type subType,
                                  FeatureTypes.Type superType)

Work out if one type is a sub-type of another.

This is the transiative closure of Type.getParent(). It will return true if superType is reachable by following getParent() calls, and false otherwise.

Parameters:

subType - the Type of the potential sub type

superType - the Type of the potential super type

Returns:

true if they are sub-super types, false otherwise