Package 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 Details

    • 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 Details

  • Method Details

    • 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