org.biojava.bio.program.unigene

Class UnigeneTools

java.lang.Object

org.biojava.bio.program.unigene.UnigeneTools

public class UnigeneTools
extends Object

Usefull tools for working with Unigene.

This class is the main port-of-call for users of the Unigene package. It provides the core APIs for finding a Unigene database as well as registering your own Unigene drivers. Additionaly, it contains methods to return parsers for each of the main Unigene flat-file types. If you wish to bypass the biojava object model entirely, you can choose to use these parsers instead.

Example use

Creating a Unigene instance from your local Unigene directory (assuming that you have read/write privileges to the directory)

 UnigeneDB unigene = UnigeneTools.createUnigene(
   new URL("file:///usr/local/biodata/unigene") );
 

Fetch a unigene cluster

 UnigeneDB unigene = UnigeneTools.loadUnigene(
   new URL("file:///usr/local/biodata/unigene") );
 UnigeneCluster cluster = unigenge.getCluster("Aga001");
 System.out.println("Title: " + cluster.getTitle());
 

Parse a data file yourself

 BufferedReader br = new BufferedReader(new FileReader(unigeneFile));
 Parser = new Parser();
 TagValueListener echo = new Echo();
 ParserListener pl = UnigeneTools.buildDataParser(echo);

 while(parser.read(br, pl.getParser(), pl.getListener())) {
   // read an entry
 }
 

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field and Description
static AnnotationType	LIBRARY_ANNOTATION Annotation schema for all Unigene libraries.
static AnnotationType	UNIGENE_ANNOTATION Annotation schema for all UnigeneCluster instances.

Constructor Summary

Constructors

Constructor and Description
UnigeneTools()

Method Summary

Modifier and Type	Method and Description
static ParserListener	buildDataParser(TagValueListener listener) Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
static ParserListener	buildLibInfoParser(TagValueListener listener) Generate a tag-value parser for the library info unigene files.
static UnigeneDB	createUnigene(URL dbURL) Create a new UnigeneDB instance referred to by a URL.
static UnigeneFactory	findFactory(URL dbURL) Find the UnigeneFactory that can accept a URL.
static String	getSpeciesForShortName(String name) Converts short species names (like Hs) to long species names (like Homo Sapiens).
static UnigeneDB	loadUnigene(URL dbURL) Load a UnigeneDB instance referred to by a URL.
static void	registerFactory(UnigeneFactory factory) Register a UnigeneFactory.
static void	unregisterFactory(UnigeneFactory factory) Register a UnigeneFactory.

Methods inherited from class java.lang.Object

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

Field Detail

UNIGENE_ANNOTATION

public static final AnnotationType UNIGENE_ANNOTATION

Annotation schema for all UnigeneCluster instances. This states what propperties can be expected to be associated with a cluster and how many values they may have.

LIBRARY_ANNOTATION

public static final AnnotationType LIBRARY_ANNOTATION

Annotation schema for all Unigene libraries. This states what propperties can be expected to be associated with a library and how many values they may have.

Constructor Detail

UnigeneTools

public UnigeneTools()

Method Detail

getSpeciesForShortName

public static String getSpeciesForShortName(String name)

Converts short species names (like Hs) to long species names (like Homo Sapiens).

Parameters:

name - the short name

Returns:

the long name

buildDataParser

public static ParserListener buildDataParser(TagValueListener listener)
                                      throws ParserException

Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.

Parameters:

listener - the TagValueListener to pass events onto

Returns:

a ParserListener that is ready to consume unigene data documents

Throws:

ParserException

buildLibInfoParser

public static ParserListener buildLibInfoParser(TagValueListener listener)
                                         throws IOException,
                                                ParserException

Generate a tag-value parser for the library info unigene files.

Parameters:

listener - the TagValueListener to pass events onto

Returns:

a ParserListener that is ready to consume unigene lib.info files

Throws:

IOException

ParserException

registerFactory

public static void registerFactory(UnigeneFactory factory)

Register a UnigeneFactory.

This method is for developers who have written their own UnigeneFactory implementations. By default, jdbc and file URLs are handled by built-in factories.

When you register a factory, it will be used for all URLs that is can accept. If a factory is registered afterwards that can accept the same URL, the first factory registered will be used.

Parameters:

factory - the UnigeneFactory to register

unregisterFactory

public static void unregisterFactory(UnigeneFactory factory)

Register a UnigeneFactory.

This method is for developers who wish to unregister a factory.

Parameters:

factory - the UnigeneFactory to unregister

loadUnigene

public static UnigeneDB loadUnigene(URL dbURL)
                             throws BioException

Load a UnigeneDB instance referred to by a URL.

Parameters:

dbURL - the URL location the database

Returns:

a UnigeneDB instance

Throws:

BioException - if there was no UnigeneFactory able to process that URL or if there was some error connecting

createUnigene

public static UnigeneDB createUnigene(URL dbURL)
                               throws BioException

Create a new UnigeneDB instance referred to by a URL.

Parameters:

dbURL - the URL location the database

Returns:

a UnigeneDB instance

Throws:

BioException - if there was no UnigeneFactory able to process that URL or if there was some error creating it

findFactory

public static UnigeneFactory findFactory(URL dbURL)
                                  throws BioException

Find the UnigeneFactory that can accept a URL.

This method is for developers only. The normal way to interact with factories is to call UnigeneTools.loadUnigene() and UnigeneTools.createUnigene()

Parameters:

dbURL - the URL to find a factory for

Returns:

the UnigeneFactory that accepts that URL

Throws:

BioException - if there is no factory for that type of URL