Package de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg

Class KeggBriteService

java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KeggBriteService
public class KeggBriteService
extends Object
Service class providing hierarchy information using the BRITE database from KEGG If a brite hierarchy is not present in the cache, it will be loaded and stored 1. the brite hierarchy file from the kegg service is downloaded and stored in cache if not present 2. the hierarchy is created if not present

  • Method Details

    • getInstance

      public static KeggBriteService getInstance()

    • getBriteHierarchy

      public BriteHierarchy getBriteHierarchy​(String briteId) throws IOException
      Returns a map between brite ids and hierarchies
      Parameters:
      briteId - e.g. br:ko00001 or br:ko01003
      Returns:
      The BriteHierarchy object which contains the map to the entries (like K01624 or K00001)
      Throws:
      IOException

    • getBriteEntryForHierarchyByID

      public HashSet<BriteEntry> getBriteEntryForHierarchyByID​(String briteId, String id) throws IOException
      Method to get all Brite Entries (Leaf nodes in the hierarchy) that match the given ID It is a convenience method.
      Parameters:
      id -
      Returns:
      All brite entries matching the given id
      Throws:
      IOException - if method was unable to download (from KEGG) or read (cached) brite file

    • getBriteEntryForHierarchyByEC

      public HashSet<BriteEntry> getBriteEntryForHierarchyByEC​(String briteId, String ec) throws IOException
      Method to get all Brite Entries (Leaf nodes in the hierarchy) that match the It is a convenience method. given EC number
      Parameters:
      ec - Number
      Returns:
      All brite entries matching the given EC number
      Throws:
      IOException - if method was unable to download (from KEGG) or read (cached) brite file

    • extractKeggKOId

      public static String extractKeggKOId​(String koString)