bio-ensembl 1.1.0

data/lib/bio-ensembl.rb

@@ -0,0 +1,65 @@
+# #
+# = bio-ensembl.rb
+#
+# Copyright::   Copyright (C) 2009 Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+#                           
+# License::     The Ruby License
+#
+# @author Jan Aerts
+# @author Francesco Strozzi
+
+module Ensembl
+  ENSEMBL_RELEASE = 60
+
+  class Session
+    attr_accessor :coord_systems
+    attr_accessor :seqlevel_id, :seqlevel_coord_system
+    attr_accessor :toplevel_id, :toplevel_coord_system
+    attr_accessor :coord_system_ids #map CS id to CS name
+    attr_accessor :seq_regions
+    attr_accessor :collection_species
+    attr_accessor :release
+
+    def initialize
+      @coord_systems = Hash.new # key = id; value = CoordSystem object
+      @coord_system_ids = Hash.new # key = id; value = name
+      @seq_regions = Hash.new
+      @release = ENSEMBL_RELEASE
+    end
+
+    def reset
+      @coord_systems = Hash.new
+      @coord_system_ids = Hash.new
+      @seq_regions = Hash.new
+      @seqlevel_id = nil
+      @toplevel_id = nil
+      @seqlevel_coord_system = nil
+      @toplevel_coord_system = nil
+      @collection_species = nil
+    end
+  end
+
+  SESSION = Ensembl::Session.new
+
+end
+
+
+
+# BioRuby
+require 'bio'
+
+# Database connection
+require 'active_record'
+require 'bio-ensembl/db_connection'
+
+# Core modules
+require 'bio-ensembl/core/activerecord'
+require 'bio-ensembl/core/transcript'
+require 'bio-ensembl/core/slice'
+require 'bio-ensembl/core/project'
+require 'bio-ensembl/core/transform'
+require 'bio-ensembl/core/collection'
+
+# Variation modules
+require 'bio-ensembl/variation/activerecord'

data/lib/bio-ensembl/core/activerecord.rb

@@ -0,0 +1,1812 @@
+#
+# = ensembl/core/activerecord.rb - ActiveRecord mappings to Ensembl core
+#
+# Copyright::   Copyright (C) 2007-2009 Jan Aerts <http://jandot.myopenid.com>
+#                                       Francesco Strozzi <francesco.strozzi@gmail.com>                                        
+# License::     The Ruby License
+#
+# @author Jan Aerts
+# @author Francesco Strozzi
+
+# == What is it?
+# The Ensembl module provides an API to the Ensembl databases
+# stored at ensembldb.ensembl.org. This is the same information that is
+# available from http://www.ensembl.org.
+#
+# The Ensembl::Core module mainly covers sequences and
+# annotations.
+# The Ensembl::Variation module covers variations (e.g. SNPs).
+# The Ensembl::Compara module covers comparative mappings
+# between species.
+#
+# == ActiveRecord
+# The Ensembl API provides a ruby interface to the Ensembl mysql databases
+# at ensembldb.ensembl.org. Most of the API is based on ActiveRecord to
+# get data from that database. In general, each table is described by a
+# class with the same name: the coord_system table is covered by the
+# CoordSystem class, the seq_region table is covered by the SeqRegion class,
+# etc. As a result, accessors are available for all columns in each table.
+# For example, the seq_region table has the following columns: seq_region_id,
+# name, coord_system_id and length. Through ActiveRecord, these column names
+# become available as attributes of SeqRegion objects:
+#   puts my_seq_region.seq_region_id
+#   puts my_seq_region.name
+#   puts my_seq_region.coord_system_id
+#   puts my_seq_region.length.to_s
+#
+# ActiveRecord makes it easy to extract data from those tables using the
+# collection of #find methods. There are three types of #find methods (e.g.
+# for the CoordSystem class):
+# a. find based on primary key in table:
+#  my_coord_system = CoordSystem.find(5)
+# b. find_by_sql:
+#  my_coord_system = CoordSystem.find_by_sql('SELECT * FROM coord_system WHERE name = 'chromosome'")
+# c. find_by_<insert_your_column_name_here>
+#  my_coord_system1 = CoordSystem.find_by_name('chromosome')
+#  my_coord_system2 = CoordSystem.find_by_rank(3)
+# To find out which find_by_<column> methods are available, you can list the
+# column names using the column_names class methods:
+#
+#  puts Ensembl::Core::CoordSystem.column_names.join("\t")
+#
+# For more information on the find methods, see
+# http://ar.rubyonrails.org/classes/ActiveRecord/Base.html#M000344
+#
+# The relationships between different tables are accessible through the
+# classes as well. For example, to loop over all seq_regions belonging to
+# a coord_system (a coord_system "has many" seq_regions):
+#   chr_coord_system = CoordSystem.find_by_name('chromosome')
+#   chr_coord_system.seq_regions.each do |seq_region|
+#     puts seq_region.name
+#   end
+# Of course, you can go the other way as well (a seq_region "belongs to"
+# a coord_system):
+#   chr4 = SeqRegion.find_by_name('4')
+#   puts chr4.coord_system.name  #--> 'chromosome'
+#
+# To find out what relationships exist for a given class, you can use the
+# #reflect_on_all_associations class methods:
+#  puts SeqRegion.reflect_on_all_associations(:has_many).collect{|a| a.name.to_s}.join("\n")
+#  puts SeqRegion.reflect_on_all_associations(:has_one).collect{|a| a.name.to_s}.join("\n")
+#  puts SeqRegion.reflect_on_all_associations(:belongs_to).collect{|a| a.name.to_s}.join("\n")
+module Ensembl
+  # The Ensembl::Core module covers the core databases from
+  # ensembldb.ensembl.org and covers mainly sequences and their annotations.
+  # For a full description of the database (and therefore the classes that
+  # are available), see http://www.ensembl.org/info/software/core/schema/index.html
+  # and http://www.ensembl.org/info/software/core/schema/schema_description.html
+  module Core
+    # The Sliceable mixin holds the get_slice method and can be included
+    # in any class that lends itself to having a position on a SeqRegion.
+    module Sliceable
+      # The Sliceable#slice method takes the coordinates on a reference
+      # and creates a Ensembl::Core::Slice object.
+      # 
+      # @return [Ensembl::Core::Slice] Ensembl::Core::Slice object
+      def slice
+        start, stop, strand = nil, nil, nil
+        
+      	if self.class == Ensembl::Core::Intron or self.class.column_names.include?('seq_region_start')
+          start = self.seq_region_start
+        end
+      	if self.class == Ensembl::Core::Intron or self.class.column_names.include?('seq_region_end')
+          stop = self.seq_region_end
+        end
+      	if self.class == Ensembl::Core::Intron or self.class.column_names.include?('seq_region_strand')
+          strand = self.seq_region_strand
+      	else #FIXME: we shouldn't do this, but can't #project if no strand given
+          strand = 1
+        end
+      
+        return Ensembl::Core::Slice.new(self.seq_region, start, stop, strand)
+      end
+      
+      # The Sliceable#seq method takes the coordinates on a reference, transforms
+      # onto the seqlevel coordinate system if necessary, and retrieves the
+      # sequence.
+      # 
+      # @return [String] sequence
+      def seq
+        return self.slice.seq
+      end
+      
+      # The Sliceable#start method is a convenience method and returns
+      # self.seq_region_start.
+      # 
+      # @return [Integer] seq_region_start
+      def start
+        return self.seq_region_start
+      end
+      
+      # The Sliceable#stop method is a convenience method and returns
+      # self.seq_region_end.
+      # 
+      # @return [Integer] seq_region_end
+      def stop
+        return self.seq_region_end
+      end
+      
+      # The Sliceable#strand method is a convenience method and returns
+      # self.seq_region_strand.
+      # 
+      # @return [Numeric] seq_region_strand
+      def strand
+        return self.seq_region_strand
+      end
+      
+      # The Sliceable#length method returns the length of the feature (based on
+      # seq_region_start and seq_region_end.
+      # 
+      # @return [Integer] Length of the slice
+      def length
+        return self.stop - self.start + 1
+      end
+      
+      # The Sliceable#project method is used to transfer coordinates from one
+      # coordinate system to another. Suppose you have a feature on a
+      # contig in human (let's say on contig AC000031.6.1.38703) and you
+      # want to know the coordinates on the chromosome. This is a
+      # projection of coordinates from a higher ranked coordinate system to
+      # a lower ranked coordinate system. Projections can also be done
+      # from a chromosome to the contig level. However, it might be possible
+      # that more than one contig has to be included and that there exist
+      # gaps between the contigs. The output of this method therefore is
+      # an _array_ of Slice and Gap objects.
+      #
+      # At the moment, projections can only be done if the two coordinate
+      # systems are linked directly in the 'assembly' table.
+      #
+      # @example
+      #  # Get a contig slice in cow and project to scaffold level
+      #  # (i.e. going from a high rank coord system to a lower rank coord
+      #  # system)
+      #  original_feature = Gene.find(85743)
+      #  target_slices = original_feature.project('scaffold')
+      #
+      # @param [String] coord_system_name Name of coordinate system to project coordinates to
+      # @return [Array<Slice,Gap>] an array consisting of Slices and, if necessary, Gaps
+      def project(coord_system_name)
+        return self.slice.project(coord_system_name)
+      end
+
+    end
+
+
+    # The CoordSystem class describes the coordinate system to which
+    # a given SeqRegion belongs. It is an interface to the coord_system
+    # table of the Ensembl mysql database.
+    #
+    # Two virtual coordinate systems exist for
+    # every species:
+    # * toplevel: the coordinate system with rank 1
+    # * seqlevel: the coordinate system that contains the seq_regions
+    #	with the sequence
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  coord_system = Ensembl::Core::CoordSystem.find_by_name('chromosome')
+    #  if coord_system == CoordSystem.toplevel
+    #	 puts coord_system.name + " is the toplevel coordinate system."
+    #  end
+    class CoordSystem < DBConnection
+      set_primary_key 'coord_system_id'
+
+      has_many :seq_regions
+
+      # The CoordSystem#toplevel? method checks if this coordinate system is the
+      # toplevel coordinate system or not.
+      # 
+      # @return [Boolean] True if coord_system is toplevel, else false.
+      def toplevel?
+        if Collection.check # When usign multi-species databases
+          return true if self == CoordSystem.find_by_rank_and_species_id(1,self.species_id)
+        else
+          return true if self == CoordSystem.find_by_rank(1)  
+        end
+        return false
+      end
+
+      # The CoordSystem#seqlevel? method checks if this coordinate system is the
+      # seqlevel coordinate system or not.
+      # 
+      # @return [Boolean] True if coord_system is seqlevel, else false.
+      def seqlevel?
+        if Collection.check # When usign multi-species databases
+           return true if self == CoordSystem.find_by_sql("SELECT * FROM coord_system WHERE attrib LIKE '%sequence_level%' AND species_id = #{self.species_id}")[0]
+        else
+           return true if self == CoordSystem.find_seqlevel
+        end
+        return false
+      end
+      
+      # The CoordSystem#find_toplevel class method returns the toplevel coordinate
+      # system.
+      # 
+      # @return [Ensembl::Core::CoordSystem] Toplevel coord_system object.
+      def find_toplevel
+        not_cached = false
+        if Ensembl::SESSION.toplevel_coord_system.nil? 
+          not_cached = true
+        elsif Collection.check
+          not_cached = true if Ensembl::SESSION.toplevel_coord_system.species_id != self.species_id
+        end
+        if not_cached
+          if Collection.check # When usign multi-species databases
+            Ensembl::SESSION.toplevel_coord_system = CoordSystem.find_by_rank_and_species_id(1,self.species_id)
+          else
+            Ensembl::SESSION.toplevel_coord_system = CoordSystem.find_by_rank(1)
+          end
+          Ensembl::SESSION.toplevel_id = Ensembl::SESSION.toplevel_coord_system.id
+          Ensembl::SESSION.coord_system_ids[Ensembl::SESSION.toplevel_coord_system.name] = Ensembl::SESSION.toplevel_id
+          Ensembl::SESSION.coord_systems[Ensembl::SESSION.toplevel_id] = Ensembl::SESSION.toplevel_coord_system
+        end
+        return Ensembl::SESSION.toplevel_coord_system
+      end
+      
+      # The CoordSystem#find_seqlevel class method returns the seqlevel coordinate
+      # system.
+      # 
+      # @return [Ensembl::Core::CoordSystem] Seqlevel coord_system object.
+      def find_seqlevel
+        not_cached = false
+        if Ensembl::SESSION.seqlevel_coord_system.nil? 
+          not_cached = true
+        elsif Collection.check # When usign multi-species databases
+          not_cached = true if Ensembl::SESSION.seqlevel_coord_system.species_id != self.species_id
+        end
+        if not_cached
+          if Collection.check
+            Ensembl::SESSION.seqlevel_coord_system = CoordSystem.find_by_sql("SELECT * FROM coord_system WHERE attrib LIKE '%sequence_level%' AND species_id = #{self.species_id}")[0]
+          else
+            Ensembl::SESSION.seqlevel_coord_system = CoordSystem.find_by_sql("SELECT * FROM coord_system WHERE attrib LIKE '%sequence_level%'")[0]
+          end  
+          Ensembl::SESSION.seqlevel_id = Ensembl::SESSION.seqlevel_coord_system.id
+          Ensembl::SESSION.coord_system_ids[Ensembl::SESSION.seqlevel_coord_system.name] = Ensembl::SESSION.seqlevel_id
+          Ensembl::SESSION.coord_systems[Ensembl::SESSION.seqlevel_id] = Ensembl::SESSION.seqlevel_coord_system
+        end
+        return Ensembl::SESSION.seqlevel_coord_system
+      end
+      
+      # The CoordSystem#find_level class method returns the seqlevel coordinate
+      # system corresponding to the name passed.
+      # 
+      # @param [String] coord_system_name Name of coordinate system
+      # @return [Ensembl::Core::CoordSystem] Coordinate system object
+      def find_level(coord_system_name)
+        if Collection.check # When usign multi-species databases
+          return CoordSystem.find_by_sql("SELECT * FROM coord_system WHERE name = '#{coord_system_name}' AND species_id = #{self.species_id}")[0]
+        else
+          return CoordSystem.find_by_name(coord_system_name)
+        end
+      end
+      
+      # The CoordSystem#find_default_by_name class method returns the
+      # coordinate system by that name with the lowest rank. Normally, a lower
+      # rank means a 'bigger' coordinate system. The 'chromosome' typically has
+      # rank 1. However, there might be more than one coordinate system with the
+      # name chromosome but with different version (e.g. in human, there is one
+      # for the NCBI36 and one for the NCBI35 version). The older version of these
+      # is typically given a high number and the one with the new version is the
+      # 'default' system.
+      # 
+      # @return [Ensembl::Core::CoordSystem] Coordinate system object
+      def self.find_default_by_name(name)
+        all_coord_systems_with_name = Ensembl::Core::CoordSystem.find_all_by_name(name)
+        if all_coord_systems_with_name.length == 1
+          return all_coord_systems_with_name[0]
+        else
+          return all_coord_systems_with_name.select{|cs| cs.attrib =~ /default_version/}[0]
+        end
+      end
+      
+      # The CoordSystem#name_with_version returns a string containing the name
+      # and version of the coordinate system. If no version is available, then
+      # just the name is returned
+      # 
+      # @return [String] Name of the coordinate system if possible including version
+      def name_with_version
+        if self.version.nil?
+          return name
+        else
+          return [name, version].join(':')
+        end
+      end
+      
+      ## Calculate the shortest path between a source coordinate system and a
+      ## target coordinate system. This can be done by looking for the
+      ## 'assembly.mapping' records in the meta_coord table.
+      ## At the moment, only direct mappings are possible. Later on, this method
+      ## should be changed to make longer paths possible.
+      ## Is used to get features for a slice object.
+      #def calculate_path(target_coord_system)
+      #  MetaCoord.find_all_by_meta_key('assembly.mapping').each do |mapping|
+      #    coord_system_names = mapping.meta_value.split(/[#|\|]/)
+      #    if coord_system_names.sort.join(';') == [self.name_with_version, target_coord_system.name_with_version].sort.join(';')
+      #      answer = Array.new
+      #      answer.push(CoordSystem.find_by_name(coord_system_names[0]))
+      #      answer.push(CoordSystem.find_by_name(coord_system_names[1]))
+      #      return answer
+      #    end
+      #  end
+      #  return nil
+      #  
+      #end
+    end
+
+    # The SeqRegion class describes a part of a coordinate systems. It is an
+    # interface to the seq_region table of the Ensembl mysql database.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  chr4 = SeqRegion.find_by_name('4')
+    #  puts chr4.coord_system.name     #--> 'chromosome'
+    #  chr4.genes.each do |gene|
+    #	 puts gene.biotype
+    #  end
+    class SeqRegion < DBConnection
+      set_primary_key 'seq_region_id'
+
+      belongs_to :coord_system
+      has_many :simple_features
+      has_many :marker_features
+      has_many :genes
+      has_many :exons
+      has_many :repeat_features
+      has_many :seq_region_attribs
+      has_many :attrib_types, :through => :seq_region_attrib
+      has_many :transcripts
+      has_one :dna
+      has_many :dna_align_features
+      has_many :misc_features
+      has_many :density_features
+      has_many :karyotypes
+      has_many :oligo_features
+      has_many :prediction_exons
+      has_many :prediction_transcripts
+      has_many :protein_align_features
+      has_many :regulatory_features
+      has_many :assembly_exceptions
+
+      # See http://blog.hasmanythrough.com/2006/4/21/self-referential-through
+      has_many :asm_links_as_asm, :foreign_key => 'asm_seq_region_id', :class_name => 'AssemblyLink'
+      has_many :asm_links_as_cmp, :foreign_key => 'cmp_seq_region_id', :class_name => 'AssemblyLink'
+      has_many :asm_seq_regions, :through => :asm_links_as_cmp
+      has_many :cmp_seq_regions, :through => :asm_links_as_asm
+
+      alias attribs seq_region_attribs
+      
+      # The SeqRegion#slice method returns a slice object that covers the whole
+      # of the seq_region.
+      #
+      # @return [Ensembl::Core::Slice] Slice object
+      def slice
+        return Ensembl::Core::Slice.new(self)
+      end
+      
+      # The SeqRegion#assembled_seq_regions returns the sequence regions on which
+      # the current region is assembled. For example, calling this method on a
+      # contig sequence region, it might return the chromosome that that contig
+      # is part of. Optionally, this method takes a coordinate system name so
+      # that only regions of that coordinate system are returned.
+      # 
+      # @param [String] coord_system_name Name of coordinate system
+      # @return [Array<SeqRegion>] Array of SeqRegion objects
+      def assembled_seq_regions(coord_system_name = nil)
+        if coord_system_name.nil?
+          return self.asm_seq_regions
+        else
+          answer = Array.new
+      	  coord_system = CoordSystem.find_by_name(coord_system_name)
+          self.asm_seq_regions.each do |asr|
+            if asr.coord_system_id == coord_system.id
+              answer.push(asr)
+            end
+          end
+      	  return answer
+        end
+      end
+
+      # The SeqRegion#component_seq_regions returns the sequence regions
+      # contained within the current region (in other words: the bits used to
+      # assemble the current region). For example, calling this method on a
+      # chromosome sequence region, it might return the contigs that were assembled
+      # into this chromosome. Optionally, this method takes a coordinate system
+      # name so that only regions of that coordinate system are returned.
+      # 
+      # @param [String] coord_system_name Name of coordinate system
+      # @return [Array<SeqRegion>] Array of SeqRegion objects
+      def component_seq_regions(coord_system_name = nil)
+      	if coord_system_name.nil?
+          return self.cmp_seq_regions
+        else
+          answer = Array.new
+      	  coord_system = CoordSystem.find_by_name(coord_system_name)
+          self.cmp_seq_regions.each do |csr|
+            if csr.coord_system_id == coord_system.id
+              answer.push(csr)
+            end
+          end
+      	  return answer
+        end
+      end
+
+      # This method queries the assembly table to find those rows (i.e.
+      # AssemblyLink objects) for which this seq_region is the assembly.
+      #
+      # @example
+      #  my_seq_region = SeqRegion.find('4')
+      #  first_link = my_seq_region.assembly_links_as_assembly[0]
+      #  puts first_link.asm_start.to_s + "\t" + first_link.asm_end.to_s
+      #
+      # @param [CoordSystem] coord_system Coordinate system object
+      #   that the components should belong to
+      # @return [Array<AssemblyLink>] Array of AssemblyLink objects
+      def assembly_links_as_assembly(coord_system = nil)
+        if Ensembl::SESSION.coord_system_ids.has_key?(coord_system.name)
+          coord_system_id = Ensembl::SESSION.coord_system_ids[coord_system.name]
+        else
+          Ensembl::SESSION.coord_systems[cs.id] = coord_system.id
+          Ensembl::SESSION.coord_system_ids[coord_system.name] = coord_system.id
+        end
+        coord_system = Ensembl::SESSION.coord_systems[coord_system.id]
+        return AssemblyLink.find_by_sql("SELECT * FROM assembly a WHERE a.asm_seq_region_id = #{self.id} AND a.cmp_seq_region_id IN (SELECT sr.seq_region_id FROM seq_region sr WHERE coord_system_id = #{coord_system.id} )")
+      end
+
+      # This method queries the assembly table to find those rows (i.e.
+      # AssemblyLink objects) for which this seq_region is the component.
+      #
+      # @example
+      #
+      #  my_seq_region = SeqRegion.find('Chr4.003.1')
+      #  first_link = my_seq_region.assembly_links_as_component[0]
+      #  puts first_link.asm_start.to_s + "\t" + first_link.asm_end.to_s
+      #
+      # @param [CoordSystem] coord_system Coordinate system object that the assembly
+      #   should belong to
+      # @return [Array<AssemblyLink>] Array of AssemblyLink objects
+      def assembly_links_as_component(coord_system = nil)
+        if coord_system.nil?
+          return self.asm_links_as_cmp
+        else
+      	  return self.asm_links_as_cmp.select{|alac| alac.asm_seq_region.coord_system_id == coord_system.id}
+        end
+      end
+
+      # The SeqRegion#sequence method returns the sequence of this seq_region. At
+      # the moment, it will only return the sequence if the region belongs to the
+      # seqlevel coordinate system.
+      #
+      # @return [String] DNA sequence
+      def sequence
+        return self.dna.sequence
+      end
+      alias seq sequence
+
+      # The SeqRegion#subsequence method returns a subsequence of this seq_region. At
+      # the moment, it will only return the sequence if the region belongs to the
+      # seqlevel coordinate system.
+      # 
+      # @param [Integer] start Start position
+      # @param [Integer] stop Stop position
+      # @return [String] DNA sequence
+      def subsequence(start, stop)
+      	return self.seq.slice(start - 1, (stop - start) + 1)
+      end
+      alias subseq subsequence
+
+    end
+
+    # The AssemblyLink class describes the relationships between different
+    # seq_regions. For example, a chromosome might consist of a number of
+    # scaffolds, each of which in turn consists of a number of contigs. The
+    # AssemblyLink class
+    # This class is an interface to the assembly table of the Ensembl mysql
+    # database.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  chr4 = SeqRegion.find_by_name('4')
+    #  puts chr4.coord_system.name     #--> 'chromosome'
+    #  chr4.genes.each do |gene|
+    #	   puts gene.biotype
+    #  end
+    class AssemblyLink < DBConnection
+      set_table_name 'assembly'
+      set_primary_key nil
+
+      # See http://blog.hasmanythrough.com/2006/4/21/self-referential-through
+      belongs_to :asm_seq_region, :foreign_key => 'asm_seq_region_id', :class_name => 'SeqRegion'
+      belongs_to :cmp_seq_region, :foreign_key => 'cmp_seq_region_id', :class_name => 'SeqRegion'
+    end
+
+    # The AssemblyException class describes the exceptions in to AssemblyLink. Most
+    # notably, this concerns the allosomes. In human, for example, only the
+    # part of the Y chromosome that is different from X is covered in the
+    # assembly table. Therefore, the sequence of the tip and end of the Y
+    # chromosome are not stored in the database, but fetched from the X
+    # chromosome. The assembly_exception table contain the information on
+    # which bits are the same.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class should normally not be used directly by the user.   
+    class AssemblyException < DBConnection
+      include Sliceable
+      
+      set_primary_key 'assembly_exception_id'
+      
+      belongs_to :seq_region
+    end
+
+    # The MetaCoord class describes what coordinate systems are used to annotate
+    # features. It will for example tell you that marker_features are annotated
+    # either on the chromosome, supercontig and clone level.
+    #
+    # This class should normally not be used by the end user, but is used internally.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class MetaCoord < DBConnection
+      set_primary_key nil
+    end
+
+    # The Meta class describes meta data of the database. These include information
+    # on what coordinate system is mapping on another one and which patches
+    # are applied.
+    #
+    # This class should normally not be used by the end user, but is used internally.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Meta < DBConnection
+      set_primary_key nil
+    end
+
+    # The Analysis class describes an analysis.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  repeat_masker_analysis = Analysis.find_by_logic_name('RepeatMask')
+    #  puts repeat_masker_analysis.to_yaml
+    class Analysis < DBConnection
+      set_primary_key 'analysis_id'
+
+      has_many :genes
+      has_many :dna_align_features
+      has_many :protein_align_features
+      has_one :analysis_description
+      has_many :density_types
+      has_many :oligo_features
+      has_many :protein_features
+      has_many :regulatory_features
+      has_many :simple_features
+      has_many :prediction_transcripts
+    end
+
+    # The AnalysisDescription class belongs to an analysis.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  descr = AnalysisDescription.find(3)
+    #  puts descr.to_yaml
+    class AnalysisDescription < DBConnection
+      set_primary_key nil
+
+      belongs_to :analysis
+    end
+
+    # The Dna class contains the actual DNA sequence for the sequence regions
+    # that belong to the seq_level coordinate system.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  seq_region = SeqRegion.find(1)
+    #  puts seq_region.dna.sequence
+    class Dna < DBConnection
+      set_primary_key nil
+
+      belongs_to :seq_region
+    end
+
+    # The Exon class describes an exon.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  seq_region = SeqRegion.find(1)
+    #  puts seq_region.exons.length
+    class Exon < DBConnection
+      include Sliceable
+
+      set_primary_key 'exon_id'
+
+      belongs_to :seq_region
+      has_many :exon_transcripts
+      has_many :transcripts, :through => :exon_transcripts
+
+      has_many :translations, :foreign_key => 'start_exon_id'
+      has_many :translations, :foreign_key => 'end_exon_id'
+
+      has_one :exon_stable_id
+
+      has_many :exon_supporting_features
+      has_many :dna_align_features, :through => :exon_supporting_features, :conditions => ["feature_type = 'dna_align_feature'"]
+      has_many :protein_align_features, :through => :exon_supporting_features, :conditions => ["feature_type = 'protein_align_feature'"]
+
+      def stable_id
+        return self.exon_stable_id.stable_id
+      end
+
+      # The Exon#seq method returns the sequence of the exon.
+      def seq
+        seq_region = nil
+        if Ensembl::SESSION.seq_regions.has_key?(self.seq_region_id)
+          seq_region = Ensembl::SESSION.seq_regions[self.seq_region_id]
+        else
+          seq_region = self.seq_region
+          Ensembl::SESSION.seq_regions[seq_region.id] = seq_region
+        end
+      	slice = Ensembl::Core::Slice.new(seq_region, seq_region_start, seq_region_end, seq_region_strand)
+        return slice.seq
+      end
+      
+      
+      def self.find_by_stable_id(stable_id)
+          exon_stable_id = ExonStableId.find_by_stable_id(stable_id)
+          if exon_stable_id.nil?
+            return nil
+          else
+            return exon_stable_id.exon
+          end
+      end
+      
+    end
+
+    # The ExonStableId class provides an interface to the exon_stable_id
+    # table. This table contains Ensembl stable IDs for exons.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  my_exon = ExonStableId.find_by_stable_id('ENSE00001494622').exon
+    class ExonStableId < DBConnection
+      set_primary_key 'stable_id'
+      
+      belongs_to :exon
+    end
+
+    # The ExonTranscript class provides the link between exons and transcripts.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  link = ExonTranscript.find(1)
+    #  puts link.exon.to_yaml
+    #  puts link.transcript.to_yaml
+    class ExonTranscript < DBConnection
+      set_primary_key nil
+
+      belongs_to :exon
+      belongs_to :transcript
+    end
+
+    class ExonSupportingFeature < DBConnection
+      set_table_name 'supporting_feature'
+      set_primary_key nil
+      
+      belongs_to :exon
+      belongs_to :dna_align_feature, :class_name => "DnaAlignFeature", :foreign_key => 'feature_id'
+      belongs_to :protein_align_feature, :class_name => "ProteinAlignFeature", :foreign_key => 'feature_id'
+    end
+    
+    class TranscriptSupportingFeature < DBConnection
+      set_primary_key nil
+      
+      belongs_to :transcript
+      belongs_to :dna_align_feature, :class_name => "DnaAlignFeature", :foreign_key => 'feature_id'
+      belongs_to :protein_align_feature, :class_name => "ProteinAlignFeature", :foreign_key => 'feature_id'
+    end
+
+    # The SimpleFeature class describes simple features that have positions
+    # on a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  simple_feature = SimpleFeature.find(123)
+    #  puts simple_feature.analysis.logic_name
+    class SimpleFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'simple_feature_id'
+
+      belongs_to :seq_region
+      belongs_to :analysis
+    end
+
+    # The DensityFeature class provides an interface to the density_feature
+    # table.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  density_feature = DensityFeature.find(2716384)
+    #  puts density_feature.to_yaml
+    class DensityFeature < DBConnection
+      set_primary_key 'density_feature_id'
+
+      belongs_to :density_type
+      belongs_to :seq_region
+    end
+
+    # The DensityType class provides an interface to the density_type
+    # table.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    class DensityType < DBConnection
+      set_primary_key 'density_type_id'
+
+      has_many :density_features
+      belongs_to :analysis
+    end
+
+    # The Marker class provides an interface to the marker
+    # table. This table contains primer sequences and PCR product lengths.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  marker = Marker.find(52194)
+    #  puts marker.left_primer
+    #  puts marker.right_primer
+    #  puts marker.min_primer_dist.to_s
+    class Marker < DBConnection
+      set_primary_key 'marker_id'
+
+      has_many :marker_features
+      has_many :marker_synonyms
+      has_many :marker_map_locations
+
+      def self.inheritance_column
+        nil
+      end
+
+      # The Marker#name method returns a comma-separated list of synonyms of
+      # this marker
+      #
+      # @example
+      #  marker = Marker.find(1)
+      #  puts marker.name    --> 58017,D29149
+      def name
+      	self.marker_synonyms.collect{|ms| ms.name}.join(',')
+      end
+
+      # The Marker#find_by_name class method returns one marker with this name.
+      #
+      # @return [Marker, nil] Marker object or nil
+      def self.find_by_name(name)
+        all_names = self.find_all_by_name(name)
+        if all_names.length == 0
+          return nil
+        else
+          return all_names[0]
+        end
+      end
+
+      # The Marker#find_all_by_name class method returns all markers with this
+      # name. If no marker is found, it returns an empty array.
+      # 
+      # @return [Array] Empty array or array of Marker objects
+      def self.find_all_by_name(name)
+      	marker_synonyms = Ensembl::Core::MarkerSynonym.find_all_by_name(name)
+        answers = Array.new
+      	marker_synonyms.each do |ms|
+          answers.push(Ensembl::Core::Marker.find_all_by_marker_id(ms.marker_id))
+        end
+      	answers.flatten!
+        return answers
+      end
+
+      #def to_mappings
+      #	output = Array.new
+      #  self.marker_features.each do |mf|
+      #    output.push(mf.slice.display_name)
+      #  end
+      #	return output.join("\n")
+      #
+      #end
+      
+    end
+
+    # The MarkerSynonym class provides an interface to the marker_synonym
+    # table. This table contains names for markers (that are themselves
+    # stored in the marker table (so Marker class)).
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  marker = Marker.find(52194)
+    #  puts marker.marker_synonym.source
+    #  puts marker.marker_synonym.name
+    class MarkerSynonym < DBConnection
+      set_primary_key 'marker_synonym_id'
+
+      belongs_to :marker
+    end
+
+    # The MarkerFeature class provides an interface to the marker_feature
+    # table. This table contains mappings of markers to a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  marker = Marker.find(52194)
+    #  puts marker.marker_feature.seq_region_start.to_s
+    #  puts marker.marker_feature.seq_region_end.to_s
+    class MarkerFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'marker_feature_id'
+
+      belongs_to :marker
+      belongs_to :seq_region
+    end
+
+    # The MiscFeature class provides an interface to the misc_feature
+    # table. The actual type of feature is stored in the MiscSet class.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  #TODO
+    class MiscFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'misc_feature_id'
+
+      belongs_to :seq_region
+      has_one :misc_feature_misc_set
+      has_many :misc_sets, :through => :misc_feature_misc_set
+
+      has_many :misc_attribs
+
+      alias attribs misc_attribs
+      
+      def self.find_by_attrib_type_value(code, value)
+        return self.find_all_by_attrib_type_value(code, value)[0]
+      end
+      
+      def self.find_all_by_attrib_type_value(code, value)
+        code_id = AttribType.find_by_code(code)
+      	misc_attribs = MiscAttrib.find_all_by_attrib_type_id_and_value(code_id, value)
+        answers = Array.new
+      	misc_attribs.each do |ma|
+          answers.push(MiscFeature.find_all_by_misc_feature_id(ma.misc_feature_id))
+        end
+      	answers.flatten!
+        return answers
+      end
+    end
+
+
+    # The MiscAttrib class provides an interface to the misc_attrib
+    # table. It is the link between MiscFeature and AttribType.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  marker = Marker.find(52194)
+    #  puts marker.marker_feature.seq_region_start.to_s
+    #  puts marker.marker_feature.seq_region_end.to_s
+    class MiscAttrib < DBConnection
+      set_primary_key nil
+
+      belongs_to :misc_feature
+      belongs_to :attrib_type
+      
+      def to_s
+        return self.attrib_type.code + ":" + self.value.to_s
+      end
+    end
+
+    # The MiscSet class provides an interface to the misc_set
+    # table. This table contains the sets to which MiscFeature objects
+    # belong.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  feature_set = MiscFeature.find(1)
+    #  puts feature_set.features.length.to_s
+    class MiscSet < DBConnection
+      set_primary_key 'misc_set_id'
+
+      has_many :misc_feature_misc_sets
+      has_many :misc_features, :through => :misc_feature_misc_set
+    end
+
+    # The MiscFeatureMiscSet class provides an interface to the
+    # misc_feature_misc_set table. This table links MiscFeature objects to
+    # their MiscSet.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  # TODO
+    class MiscFeatureMiscSet < DBConnection
+      set_primary_key nil
+
+      belongs_to :misc_feature
+      belongs_to :misc_set
+    end
+
+    # The Gene class provides an interface to the gene
+    # table. This table contains mappings of genes to a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  puts Gene.find_by_biotype('protein_coding').length
+    class Gene < DBConnection
+      include Sliceable
+
+      set_primary_key 'gene_id'
+
+      belongs_to :seq_region
+      has_one :gene_stable_id
+
+      has_many :gene_attribs
+      has_many :attrib_types, :through => :gene_attrib
+
+      has_many :transcripts
+
+      belongs_to :analysis
+      
+      has_many :object_xrefs, :foreign_key => 'ensembl_id', :conditions => "ensembl_object_type = 'Gene'"
+      has_many :xrefs, :through => :object_xrefs
+
+      alias attribs gene_attribs
+
+      # The Gene#stable_id method returns the stable_id of the gene (i.e. the
+      # ENSG id).
+      def stable_id
+        return self.gene_stable_id.stable_id
+      	
+      end
+
+      # The Gene#display_label method returns the default name of the gene.
+      def display_label
+        return Xref.find(self.display_xref_id).display_label
+      end
+      alias :display_name :display_label
+      alias :label :display_label
+      alias :name :display_label
+
+      # The Gene#find_all_by_name class method searches the Xrefs for that name
+      # and returns an array of the corresponding Gene objects. If the name is
+      # not found, it returns an empty array.
+      def self.find_all_by_name(name)
+      	answer = Array.new
+        xrefs = Ensembl::Core::Xref.find_all_by_display_label(name)
+        xrefs.each do |xref|
+          answer.push(Ensembl::Core::Gene.find_by_display_xref_id(xref.xref_id))
+        end
+        
+        answer.reject!{|a| a.nil?}
+      	return answer
+      end
+      
+      # The Gene#find_by_name class method searches the Xrefs for that name
+      # and returns one Gene objects (even if there should be more). If the name is
+      # not found, it returns nil.
+      def self.find_by_name(name)
+        all_names = self.find_all_by_name(name)
+        if all_names.length == 0
+          return nil
+        else
+          return all_names[0]
+        end
+      end
+      
+      # The Gene#find_by_stable_id class method fetches a Gene object based on
+      # its stable ID (i.e. the "ENSG" accession number). If the name is
+      # not found, it returns nil.
+      def self.find_by_stable_id(stable_id)
+        result = nil
+        if stable_id.kind_of? Array
+          gene_stable_ids = GeneStableId.where({:stable_id => stable_id})
+          result = (gene_stable_ids.size == 0) ? nil : gene_stable_ids.map {|id| id.gene}
+        else
+          gene_stable_id = GeneStableId.find_by_stable_id(stable_id)
+          result = (gene_stable_id.nil?) ? nil : gene_stable_id.gene
+        end
+        return result
+      end
+      
+      # The Gene#all_xrefs method is a convenience method in that it combines
+      # three methods into one. It collects all xrefs for the gene itself, plus
+      # all xrefs for all transcripts for the gene, and all xrefs for all
+      # translations for those transcripts.
+      def all_xrefs
+        answer = Array.new
+        answer.push(self.xrefs)
+        self.transcripts.each do |transcript|
+          answer.push(transcript.xrefs)
+          if ! transcript.translation.nil?
+            answer.push(transcript.translation.xrefs)
+          end
+        end
+        answer.flatten!
+        return answer
+      end
+      
+      # The Gene#go_terms method returns all GO terms associated with a gene.
+      def go_terms
+        go_db_id = ExternalDb.find_by_db_name('GO').id
+        return self.all_xrefs.select{|x| x.external_db_id == go_db_id}.collect{|x| x.dbprimary_acc}.uniq
+      end
+      
+      # The Gene#hgnc returns the HGNC symbol for the gene.
+      def hgnc
+        hgnc_db_id = ExternalDb.find_by_db_name('HGNC_curated_gene').id
+        xref = self.all_xrefs.select{|x| x.external_db_id == hgnc_db_id}[0]
+        return nil if xref.nil?
+        return xref.display_label
+      end
+
+    end
+    
+    # The Gene#canonical_transcript returns the longest transcript for that gene.
+    #
+    def canonical_transcript
+     ct = self.transcripts.sort {|a,b| b.seq.length <=> a.seq.length}
+     return ct[0]
+    end
+
+    # The GeneStableId class provides an interface to the gene_stable_id
+    # table. This table contains Ensembl stable IDs for genes.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  my_gene = GeneStableId.find_by_stable_id('ENSBTAG00000011670').gene
+    class GeneStableId < DBConnection
+      set_primary_key 'stable_id'
+
+      belongs_to :gene
+    end
+
+    # The MarkerMapLocation class provides an interface to the
+    # marker_map_location table. This table contains mappings of
+    # MarkerSynonym objects to a chromosome, and basically just stores
+    # the genetic maps.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  marker_synonym = MarkerSynonym.find_by_name('CYP19A1_(5)')
+    #  marker_synonym.marker_map_locations.each do |mapping|
+    #	 puts mapping.chromosome_name + "\t" + mapping.position.to_s
+    #  end
+    class MarkerMapLocation < DBConnection
+      set_primary_key nil
+
+      belongs_to :map
+      belongs_to :marker
+      
+    end
+
+    # The Map class provides an interface to the map
+    # table. This table contains genetic maps.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  map = Map.find_by_name('MARC')
+    #  puts map.markers.length.to_s
+    class Map < DBConnection
+      set_primary_key 'map_id'
+
+      has_many :marker_map_locations
+      has_many :markers, :through => :marker_map_locations
+
+      def name
+      	return self.map_name
+      end
+    end
+
+    # The RepeatConsensus class provides an interface to the repeat_consensus
+    # table. This table contains consensus sequences for repeats.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  repeat = RepeatFeature.find(29)
+    #  puts repeat.repeat_consensus.repeat_name + "\t" + repeat.repeat_consensus.repeat_consensus
+    class RepeatConsensus < DBConnection
+      set_primary_key 'repeat_consensus_id'
+
+      has_many :repeat_features
+    end
+
+    # The RepeatFeature class provides an interface to the repeat_feature
+    # table. This table contains mappings of repeats to a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  repeat_feature = RepeatFeature.find(29)
+    #  puts repeat_feature.seq_region_start.to_s
+    class RepeatFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'repeat_feature_id'
+
+      belongs_to :repeat_consensus
+      belongs_to :seq_region
+    end
+
+    # The SeqRegionAttrib class provides an interface to the seq_region_attrib
+    # table. This table contains attribute values for SeqRegion objects
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  chr4 = SeqRegion.find_by_name('4')
+    #  chr4.seq_region_attribs.each do |attrib|
+    #	 puts attrib.attrib_type.name + "\t" + attrib.value.to_s
+    #  end
+    class SeqRegionAttrib < DBConnection
+      set_primary_key nil
+
+      belongs_to :seq_region
+      belongs_to :attrib_type
+    end
+
+    # The GeneAttrib class provides an interface to the gene_attrib
+    # table. This table contains attribute values for Gene objects
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  #TODO
+    class GeneAttrib < DBConnection
+      set_primary_key nil
+
+      belongs_to :gene
+      belongs_to :attrib_type
+    end
+
+    # The AttribType class provides an interface to the attrib_type
+    # table. This table contains the types that attributes can belong to for
+    # SeqRegion, Gene and Transcript.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  #TODO
+    class AttribType < DBConnection
+      set_primary_key 'attrib_type_id'
+
+      has_many :seq_region_attribs
+      has_many :seq_regions, :through => :seq_region_attrib
+
+      has_many :gene_attribs
+      has_many :genes, :through => :gene_attrib
+
+      has_many :transcript_attribs
+      has_many :transcripts, :through => :transcript_attrib
+    end
+
+    # The Transcript class provides an interface to the transcript_stable_id
+    # table. This table contains the Ensembl stable IDs for Transcript
+    # objects.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  transcript_stable_id = TranscriptStableId.find_by_stable_id('ENSBTAT00000015494')
+    #  puts transcript_stable_id.transcript.to_yaml
+    class TranscriptStableId < DBConnection
+      set_primary_key 'stable_id'
+
+      belongs_to :transcript
+    end
+
+    # The TranscriptAttrib class provides an interface to the transcript_attrib
+    # table. This table contains the attributes for Transcript objects.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  transcript = Transcript.find(32495)
+    #  transcript.transcript_attribs.each do |attr|
+    #	 puts attr.attrib_type.name + "\t" + attr.value
+    #  end
+    class TranscriptAttrib < DBConnection
+      set_primary_key nil
+
+      belongs_to :transcript
+      belongs_to :attrib_type
+    end
+
+    # The DnaAlignFeature class provides an interface to the
+    # dna_align_feature table. This table contains sequence similarity
+    # mappings against a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  unigene_scan = Analysis.find_by_logic_name('Unigene')
+    #  unigene_scan.dna_align_features.each do |hit|
+    #	 puts hit.seq_region.name + "\t" + hit.hit_name + "\t" + hit.cigar_line
+    #  end
+    class DnaAlignFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'dna_align_feature_id'
+
+      belongs_to :seq_region
+      belongs_to :analysis
+      
+      has_many :exon_supporting_features
+      has_many :protein_supporting_features
+    end
+
+    # The Translation class provides an interface to the
+    # translation table. This table contains the translation start and
+    # stop positions and exons for a given Transcript
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  #TODO
+    class Translation < DBConnection
+      set_primary_key 'translation_id'
+
+      belongs_to :transcript
+      has_many :translation_stable_ids
+
+      has_many :translation_attribs
+      has_many :protein_features
+      
+      has_one :translation_stable_id
+      
+      has_many :object_xrefs, :foreign_key => 'ensembl_id', :conditions => "ensembl_object_type = 'Translation'"
+      has_many :xrefs, :through => :object_xrefs
+      
+      belongs_to :start_exon, :class_name => 'Exon', :foreign_key => 'start_exon_id'
+      belongs_to :end_exon, :class_name => 'Exon', :foreign_key => 'end_exon_id'
+
+      alias attribs translation_attribs
+      
+      # The Translation#stable_id method returns the stable ID of the translation.
+      # 
+      # @return [String] Ensembl stable ID
+      def stable_id
+      	return self.translation_stable_id.stable_id
+      end
+
+      # The Translation#display_label method returns the default name of the translation.
+      def display_label
+        return Xref.find(self.display_xref_id).display_label
+      end
+      alias :display_name :display_label
+      alias :label :display_label
+      alias :name :display_label
+
+      # The Translation#find_by_stable_id class method fetches a Translation
+      # object based on its stable ID (i.e. the "ENSP" accession number). If the 
+      # name is not found, it returns nil.
+      def self.find_by_stable_id(stable_id)
+        translation_stable_id = TranslationStableId.find_by_stable_id(stable_id)
+        if translation_stable_id.nil?
+          return nil
+        else
+          return translation_stable_id.translation
+        end
+      end
+    end
+
+    # The TranslationStableId class provides an interface to the
+    # translation_stable_id table. This table contains the Ensembl stable IDs
+    # for a given Translation.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  stable_id = TranslationStableId.find_by_name('ENSBTAP00000015494')
+    #  puts stable_id.to_yaml
+    class TranslationStableId < DBConnection
+      set_primary_key 'stable_id'
+
+      belongs_to :translation
+    end
+
+    # The TranslationAttrib class provides an interface to the
+    # translation_attrib table. This table contains attribute values for the
+    # Translation class.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  translation = Translation.find(9979)
+    #  translation.translation_attribs.each do |attr|
+    #	 puts attr.attr_type.name + "\t" + attr.value
+    #  end
+    class TranslationAttrib < DBConnection
+      set_primary_key nil
+
+      belongs_to :translation
+      belongs_to :attrib_type
+    end
+
+    # The Xref class provides an interface to the
+    # xref table. This table contains external references for objects in the
+    # database.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  gene = Gene.find(1)
+    #  gene.xrefs.each do |xref|
+    #	   puts xref.display_label + "\t" + xref.description
+    #  end
+    class Xref < DBConnection
+      set_primary_key 'xref_id'
+
+      belongs_to :external_db
+      has_many :external_synonyms
+
+      has_many :genes
+      
+      def to_s
+        return self.external_db.db_name.to_s + ":" + self.display_label
+      end
+    end
+
+    # The ObjectXref class provides the link between gene, transcript and
+    # translation objects on the one hand and an xref on the other.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  gene = Gene.find(1)
+    #  gene.object_xrefs.each do |ox|
+    #	   puts ox.to_yaml
+    #  end
+    class ObjectXref < DBConnection
+      set_primary_key 'object_xref_id'
+      
+      belongs_to :gene, :class_name => "Gene", :foreign_key => 'ensembl_id', :conditions => ["ensembl_object_type = 'Gene'"]
+      belongs_to :transcript, :class_name => "Transcript", :foreign_key => 'ensembl_id', :conditions => ["ensembl_object_type = 'Transcript'"]
+      belongs_to :translation, :class_name => "Translation", :foreign_key => 'ensembl_id', :conditions => ["ensembl_object_type = 'Translation'"]
+      belongs_to :xref
+      has_one :go_xref
+    end
+    
+    # The GoXref class provides an interface to the
+    # go_xref table. This table contains the evidence codes for those object_refs
+    # that are GO terms.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class GoXref < DBConnection
+      set_primary_key nil
+      
+      belongs_to :xref
+    end
+
+    # The ExternalDb class provides an interface to the
+    # external_db table. This table contains references to databases to which
+    # xrefs can point to
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  embl_db = ExternalDb.find_by_db_name('EMBL')
+    #  puts embl_db.xrefs.length.to_s
+    class ExternalDb < DBConnection
+      set_primary_key 'external_db_id'
+
+      has_many :xrefs
+
+      def self.inheritance_column
+        nil
+      end
+
+      # The ExternalDb#find_all_by_display_label method returns all external
+      # databases that have this label. There should normally be no more than
+      # one. If no databases are found with this name, this method returns an
+      # empty array.
+      def self.find_all_by_display_label(label)
+      	answer = Array.new
+        xrefs = Xref.find_all_by_display_label(label)
+      	xrefs.each do |xref|
+          answer.push(self.class.find_by_xref_id(xref.xref_id))
+        end
+
+        return answer
+      end
+      
+      # The ExternalDb#find_by_display_label method returns a
+      # database that has this label. If no databases are found with this name,
+      # this method returns nil.
+      # empty array.
+      def self.find_by_display_label(label)
+        all_dbs = self.find_all_by_display_label(label)
+        if all_dbs.length == 0
+          return nil
+        else
+          return all_dbs[0]
+        end
+      end
+
+      
+    end
+
+    # The ExternalSynonym class provides an interface to the
+    # external_synonym table. This table contains synonyms for Xref objects.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  xref = Xref.find(185185)
+    #  puts xref.external_synonyms[0].synonyms
+    class ExternalSynonym < DBConnection
+      set_primary_key nil
+
+      belongs_to :xref
+    end
+
+    # The Karyotype class provides an interface to the
+    # karyotype table. This table contains <>.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  band = Karyotype.find_by_band('p36.32')
+    #  puts band.to_yaml
+    class Karyotype < DBConnection
+      include Sliceable
+
+      set_primary_key 'karyotype_id'
+
+      belongs_to :seq_region
+    end
+
+    # The OligoFeature class provides an interface to the
+    # oligo_feature table. This table contains mappings of Oligo objects to
+    # a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  seq_region = SeqRegion.find_by_name('4')
+    #  puts seq_region.oligo_features.length
+    class OligoFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'oligo_feature_id'
+
+      belongs_to :seq_region
+      belongs_to :oligo_probe
+      belongs_to :analysis
+    end
+
+    # The OligoProbe class provides an interface to the
+    # oligo_probe table.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  probe = OligoProbe.find_by_name('373:434;')
+    #  puts probe.probeset + "\t" + probe.oligo_array.name
+    class OligoProbe < DBConnection
+      set_primary_key 'oligo_probe_id'
+
+      has_many :oligo_features
+      belongs_to :oligo_array
+    end
+
+    # The OligoArray class provides an interface to the
+    # oligo_array table. This table contains data describing a microarray
+    # slide.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  array = OligoArray.find_by_name_and_type('Bovine','AFFY')
+    #  puts array.oligo_probes.length
+    class OligoArray < DBConnection
+      set_primary_key 'oligo_array_id'
+
+      has_many :oligo_probes
+    end
+
+    # The PredictionExon class provides an interface to the
+    # prediction_exon table. This table contains <>.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  #TODO
+    class PredictionExon < DBConnection
+      include Sliceable
+
+      set_primary_key 'prediction_exon_id'
+
+      belongs_to :prediction_transcript
+      belongs_to :seq_region
+    end
+
+    # The PredictionTranscript class provides an interface to the
+    # prediction_transcript table.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  predicted_transcript = PredictionTranscript.find_by_display_label('GENSCAN00000000006')
+    #  puts predicted_transcript.prediction_exons.length
+    class PredictionTranscript < DBConnection
+      include Sliceable
+
+      set_primary_key 'prediction_transcript_id'
+
+      has_many :prediction_exons
+      belongs_to :seq_region
+      belongs_to :analysis
+    end
+
+    # The ProteinFeature class provides an interface to the
+    # protein_feature table. This table contains mappings of a Translation
+    # onto a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  #TODO
+    class ProteinFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'protein_feature_id'
+
+      belongs_to :translation
+      belongs_to :analysis
+    end
+
+    # The ProteinAlignFeature class provides an interface to the
+    # protein_align_feature table. This table contains sequence similarity
+    # mappings against a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  uniprot_scan = Analysis.find_by_logic_name('Uniprot')
+    #  uniprot_scan.protein_align_features.each do |hit|
+    #	 puts hit.seq_region.name + "\t" + hit.hit_name + "\t" + hit.cigar_line
+    #  end
+    class ProteinAlignFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'protein_align_feature_id'
+
+      belongs_to :seq_region
+      belongs_to :analysis
+      
+      has_many :exon_supporting_features
+      has_many :transcript_supporting_features
+    end
+
+    # The RegulatoryFactor class provides an interface to the
+    # regulatory_factor table.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  factor = RegulatoryFactor.find_by_name('crtHsap8070')
+    #  puts factor.to_yaml
+    class RegulatoryFactor < DBConnection
+      set_primary_key 'regulatory_factor_id'
+
+      has_many :regulatory_features
+    end
+
+    # The RegulatoryFeature class provides an interface to the
+    # regulatory_feature table. This table contains mappings of
+    # RegulatoryFactor objects against a SeqRegion.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # This class includes the mixin Sliceable, which means that it is mapped
+    # to a SeqRegion object and a Slice can be created for objects of this
+    # class. See Sliceable and Slice for more information.
+    #
+    # @example
+    #  analysis = Analysis.find_by_logic_name('miRanda')
+    #  analysis.regulatory_features.each do |feature|
+    #	 puts feature.name + "\t" + feature.regulatory_factor.name
+    #  end
+    class RegulatoryFeature < DBConnection
+      include Sliceable
+
+      set_primary_key 'regulatory_feature_id'
+
+      belongs_to :seq_region
+      belongs_to :analysis
+      belongs_to :regulatory_factor
+    end
+  end
+end