bio 1.0.0 → 1.1.0

data/lib/bio/io/registry.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2002, 2003, 2004, 2005
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     LGPL
+# License::     The Ruby License
 #
-# $Id: registry.rb,v 1.16 2005/12/18 15:58:42 k Exp $
+# $Id: registry.rb,v 1.19 2007/04/05 23:35:41 trevor Exp $
 #
 # == Description
 #
@@ -81,26 +81,10 @@
 # * http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/?cvsroot=obf-common
 # * http://www.open-bio.org/registry/seqdatabase.ini
 #
-#--
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
-#
 
 require 'uri'
 require 'net/http'
+require 'bio/command'
 
 
 module Bio
@@ -187,7 +171,7 @@ class Registry
 
   def read_remote(url)
     schema, user, host, port, reg, path, = URI.split(url)
-    Net::HTTP.start(host, port) do |http|
+    Bio::Command.start_http(host, port) do |http|
       response, = http.get(path)
       parse_stanza(response.body)
     end

data/lib/bio/io/soapwsdl.rb

@@ -2,14 +2,18 @@
 # = bio/io/soapwsdl.rb - SOAP/WSDL interface class
 #
 # Copyright::   Copyright (C) 2004 
-#               KATAYAMA Toshiaki <k@bioruby.org>
-# License::     LGPL
-#
-# $Id: soapwsdl.rb,v 1.3 2005/12/18 16:51:18 nakao Exp $
-#
-# SOAP/WSDL 
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
 #
+# $Id: soapwsdl.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
 #
+begin
+  require 'soap/wsdlDriver'
+rescue LoadError
+end
+
+module Bio
+
 # == Examples
 # 
 # class API < Bio::SOAPWSDL
@@ -26,48 +30,24 @@
 # (case might be insensitive) as required by SOAP4R.
 #
 # --- soap_use_proxy
+#
 # Set the value of this variable to 'on'.
 #
 # --- http_proxy
+#
 # Set the URL of your proxy server (http://myproxy.com:8080 etc.).
 #
-# === Example
+# === Example to use HTTP proxy
 # 
 # % export soap_use_proxy=on
 # % export http_proxy=http://localhost:8080
 #
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
-#
-
-begin
-  require 'soap/wsdlDriver'
-rescue LoadError
-end
-
-module Bio
-
 class SOAPWSDL
 
-  # WSDL URL
+  # Returns URL of the current WSDL file.
   attr_reader :wsdl
 
-  # log IO
+  # Returns current logging IO.
   attr_reader :log
 
 
@@ -89,26 +69,51 @@ class SOAPWSDL
   private :create_driver
 
 
-  # Set a WSDL URL.
+  # Change the URL for WSDL file
+  #
+  #   serv = Bio::SOAPWSDL.new("http://soap.genome.jp/KEGG.wsdl")
+  #
+  # or
+  # 
+  #   serv = Bio::SOAPWSDL.new
+  #   serv.wsdl = "http://soap.genome.jp/KEGG.wsdl"
+  #
+  # Note that you can't read two or more different WSDL files at once.
+  # In that case, create Bio::SOAPWSDL object for each.
+  #
   def wsdl=(url)
     @wsdl = url
     create_driver
   end
 
 
-  # Set log IO
+  # Change the IO for logging.  The argument is passed to wiredump_dev method
+  # of the SOAP4R, thus
+  #
+  #   serv = Bio::SOAPWSDL.new
+  #   serv.log = STDERR
+  #
+  # will print all the SOAP transactions in standard error.
+  # This feature is especially useful for debug.
+  #
   def log=(io)
     @log = io
     @driver.wiredump_dev = @log
   end
 
 
+  # List of methods defined by WSDL
+  def list_methods
+    @driver.methods(false)
+  end
+
+
   def method_missing(*arg)
     @driver.send(*arg)
   end
   private :method_missing
 
-end # SOAP
+end # SOAPWSDL
 
 end # Bio
 

data/lib/bio/io/sql.rb

@@ -1,23 +1,11 @@
 #
-# bio/io/sql.rb - BioSQL access module
+# = bio/io/sql.rb - BioSQL access module
 #
-#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2002 Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2006 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: sql.rb,v 1.4 2005/09/26 13:04:28 k Exp $
+# $Id: sql.rb,v 1.8 2007/04/05 23:35:41 trevor Exp $
 #
 
 begin
@@ -30,293 +18,304 @@ require 'bio/feature'
 
 module Bio
 
-  class SQL
+class SQL
 
-    def initialize(db = 'dbi:Mysql:biosql', user = nil, pass = nil)
-      @dbh = DBI.connect(db, user, pass)
-    end
+  def initialize(db = 'dbi:Mysql:biosql', user = nil, pass = nil)
+    @dbh = DBI.connect(db, user, pass)
+  end
 
-    def close
-      @dbh.disconnect
-    end
+  def close
+    @dbh.disconnect
+  end
 
-    def fetch(accession)	# or display_id for fall back
-      query = "select * from bioentry where accession = ?"
-      entry = @dbh.execute(query, accession).fetch
-      return Sequence.new(@dbh, entry) if entry
+  # Returns Bio::SQL::Sequence object.
+  def fetch(accession)	# or display_id for fall back
+    query = "select * from bioentry where accession = ?"
+    entry = @dbh.execute(query, accession).fetch
+    return Sequence.new(@dbh, entry) if entry
 
-      query = "select * from bioentry where display_id = ?"
-      entry = @dbh.execute(query, accession).fetch
-      return Sequence.new(@dbh, entry) if entry
-    end
-    alias get_by_id fetch
+    query = "select * from bioentry where display_id = ?"
+    entry = @dbh.execute(query, accession).fetch
+    return Sequence.new(@dbh, entry) if entry
+  end
+  alias get_by_id fetch
 
 
-    # for lazy fetching
+  # for lazy fetching
 
-    class Sequence
+  class Sequence
 
-      def initialize(dbh, entry)
-        @dbh = dbh
-        @bioentry_id = entry['bioentry_id']
-        @database_id = entry['biodatabase_id']
-        @entry_id = entry['display_id']
-        @accession = entry['accession']
-        @version = entry['entry_version']
-        @division = entry['division']
-      end
-      attr_reader :accession, :division, :entry_id, :version
+    def initialize(dbh, entry)
+      @dbh = dbh
+      @bioentry_id = entry['bioentry_id']
+      @database_id = entry['biodatabase_id']
+      @entry_id = entry['display_id']
+      @accession = entry['accession']
+      @version = entry['entry_version']
+      @division = entry['division']
+    end
+    attr_reader :accession, :division, :entry_id, :version
 
 
-      def to_fasta
-        if seq = seq
-          return seq.to_fasta(@accession)
-        end
+    def to_fasta
+      if seq = seq
+        return seq.to_fasta(@accession)
       end
+    end
 
-      def seq
-        query = "select * from biosequence where bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        return unless row
+    # Returns Bio::Sequence::NA or AA object.
+    def seq
+      query = "select * from biosequence where bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      return unless row
 
-        mol = row['molecule']
-        seq = row['biosequence_str']
+      mol = row['alphabet']
+      seq = row['seq']
 
-        case mol
-        when /.na/i			# 'dna' or 'rna'
-          Bio::Sequence::NA.new(seq)
-        else				# 'protein'
-          Bio::Sequence::AA.new(seq)
-        end
+      case mol
+      when /.na/i			# 'dna' or 'rna'
+        Bio::Sequence::NA.new(seq)
+      else				# 'protein'
+        Bio::Sequence::AA.new(seq)
       end
+    end
 
-      def subseq(from, to)
-        length = to - from + 1
-        query = "select molecule, substring(biosequence_str, ?, ?) as subseq" +
-                " from biosequence where bioentry_id = ?"
-        row = @dbh.execute(query, from, length, @bioentry_id).fetch
-        return unless row
-
-        mol = row['molecule']
-        seq = row['subseq']
-
-        case mol
-        when /.na/i			# 'dna' or 'rna'
-          Bio::Sequence::NA.new(seq)
-        else				# 'protein'
-          Bio::Sequence::AA.new(seq)
-        end
+    # Returns Bio::Sequence::NA or AA object (by lazy fetching).
+    def subseq(from, to)
+      length = to - from + 1
+      query = "select alphabet, substring(seq, ?, ?) as subseq" +
+              " from biosequence where bioentry_id = ?"
+      row = @dbh.execute(query, from, length, @bioentry_id).fetch
+      return unless row
+
+      mol = row['alphabet']
+      seq = row['subseq']
+
+      case mol
+      when /.na/i			# 'dna' or 'rna'
+        Bio::Sequence::NA.new(seq)
+      else				# 'protein'
+        Bio::Sequence::AA.new(seq)
       end
+    end
 
 
-      def features
-        array = []
-        query = "select * from seqfeature where bioentry_id = ?"
-        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
-          next unless row
-
-          f_id = row['seqfeature_id']
-          k_id = row['seqfeature_key_id']
-          s_id = row['seqfeature_source_id']
-          rank = row['seqfeature_rank'].to_i - 1
+    # Returns Bio::Features object.
+    def features
+      array = []
+      query = "select * from seqfeature where bioentry_id = ?"
+      @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+        next unless row
 
-          # key : type (gene, CDS, ...)
-          type = feature_key(k_id)
+        f_id = row['seqfeature_id']
+        k_id = row['type_term_id']
+        s_id = row['source_term_id']
+        rank = row['rank'].to_i - 1
 
-          # source : database (EMBL/GenBank/SwissProt)
-          database = feature_source(s_id)
+        # key : type (gene, CDS, ...)
+        type = feature_key(k_id)
 
-          # location : position
-          locations = feature_locations(f_id)
+        # source : database (EMBL/GenBank/SwissProt)
+        database = feature_source(s_id)
 
-          # qualifier
-          qualifiers = feature_qualifiers(f_id)
-  
-          # rank
-          array[rank] = Bio::Feature.new(type, locations, qualifiers)
-        end
-        return Bio::Features.new(array)
-      end
+        # location : position
+        locations = feature_locations(f_id)
 
+        # qualifier
+        qualifiers = feature_qualifiers(f_id)
 
-      def references
-        array = []
-        query = <<-END
-          select * from bioentry_reference, reference
-          where bioentry_id = ? and
-          bioentry_reference.reference_id = reference.reference_id
-        END
-        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
-          next unless row
-
-          hash = {
-            'start'	=> row['reference_start'],
-            'end'	=> row['reference_end'],
-            'journal'	=> row['reference_location'],
-            'title'	=> row['reference_title'],
-            'authors'	=> row['reference_authors'],
-            'medline'	=> row['reference_medline']
-          }
-          hash.default = ''
-
-          rank = row['reference_rank'].to_i - 1
-          array[rank] = hash
-        end
-        return array
+        # rank
+        array[rank] = Bio::Feature.new(type, locations, qualifiers)
       end
+      return Bio::Features.new(array)
+    end
 
 
-      def comment
-        query = "select * from comment where bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        row ? row['comment_text'] : ''
+    # Returns reference informations in Array of Hash (not Bio::Reference).
+    def references
+      array = []
+      query = <<-END
+        select * from bioentry_reference, reference
+        where bioentry_id = ? and
+        bioentry_reference.reference_id = reference.reference_id
+      END
+      @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+        next unless row
+
+        hash = {
+          'start'	=> row['start_pos'],
+          'end'		=> row['end_pos'],
+          'journal'	=> row['location'],
+          'title'	=> row['title'],
+          'authors'	=> row['authors'],
+          'medline'	=> row['crc']
+        }
+        hash.default = ''
+
+        rank = row['rank'].to_i - 1
+        array[rank] = hash
       end
+      return array
+    end
 
-      def comments
-        array = []
-        query = "select * from comment where bioentry_id = ?"
-        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
-          next unless row
-          rank = row['comment_rank'].to_i - 1
-          array[rank] = row['comment_text']
-        end
-        return array
-      end
 
-      def database
-        query = "select * from biodatabase where biodatabase_id = ?"
-        row = @dbh.execute(query, @database_id).fetch
-        row ? row['name'] : ''
-      end
+    # Returns the first comment.  For complete comments, use comments method.
+    def comment
+      query = "select * from comment where bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      row ? row['comment_text'] : ''
+    end
 
-      def date
-        query = "select * from bioentry_date where bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        row ? row['date'] : ''
+    # Returns comments in an Array of Strings.
+    def comments
+      array = []
+      query = "select * from comment where bioentry_id = ?"
+      @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+        next unless row
+        rank = row['rank'].to_i - 1
+        array[rank] = row['comment_text']
       end
+      return array
+    end
 
-      def dblink
-        query = "select * from bioentry_direct_links where source_bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        row ? [row['dbname'], row['accession']] : []
-      end
+    def database
+      query = "select * from biodatabase where biodatabase_id = ?"
+      row = @dbh.execute(query, @database_id).fetch
+      row ? row['name'] : ''
+    end
 
-      def definition
-        query = "select * from bioentry_description where bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        row ? row['description'] : ''
-      end
+    def date
+      query = "select * from bioentry_date where bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      row ? row['date'] : ''
+    end
 
-      def keyword
-        query = "select * from bioentry_keywords where bioentry_id = ?"
-        row = @dbh.execute(query, @bioentry_id).fetch
-        row ? row['keywords'] : ''
-      end
+    def dblink
+      query = "select * from bioentry_direct_links where source_bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      row ? [row['dbname'], row['accession']] : []
+    end
 
-      def taxonomy
-        query = <<-END
-          select full_lineage, common_name, ncbi_taxa_id
-          from bioentry_taxa, taxa
-          where bioentry_id = ? and bioentry_taxa.taxa_id = taxa.taxa_id
-        END
-        row = @dbh.execute(query, @bioentry_id).fetch
-        @lineage = row ? row['full_lineage'] : ''
-        @common_name = row ? row['common_name'] : ''
-        @ncbi_taxa_id = row ? row['ncbi_taxa_id'] : ''
-        row ? [@lineage, @common_name, @ncbi_taxa_id] : []
-      end
+    def definition
+      query = "select * from bioentry_description where bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      row ? row['description'] : ''
+    end
 
-      def lineage
-        taxonomy unless @lineage
-        return @lineage
-      end
+    def keyword
+      query = "select * from bioentry_keywords where bioentry_id = ?"
+      row = @dbh.execute(query, @bioentry_id).fetch
+      row ? row['keywords'] : ''
+    end
 
-      def common_name
-        taxonomy unless @common_name
-        return @common_name
-      end
+    # Use lineage, common_name, ncbi_taxa_id methods to extract in detail.
+    def taxonomy
+      query = <<-END
+        select taxon_name.name, taxon.ncbi_taxon_id from bioentry
+        join taxon_name using(taxon_id) join taxon using (taxon_id)
+        where bioentry_id = ?
+      END
+      row = @dbh.execute(query, @bioentry_id).fetch
+#     @lineage = row ? row['full_lineage'] : ''
+      @common_name = row ? row['name'] : ''
+      @ncbi_taxa_id = row ? row['ncbi_taxon_id'] : ''
+      row ? [@lineage, @common_name, @ncbi_taxa_id] : []
+    end
 
-      def ncbi_taxa_id
-        taxonomy unless @ncbi_taxa_id
-        return @ncbi_taxa_id
-      end
+    def lineage
+      taxonomy unless @lineage
+      return @lineage
+    end
 
+    def common_name
+      taxonomy unless @common_name
+      return @common_name
+    end
 
-      private
+    def ncbi_taxa_id
+      taxonomy unless @ncbi_taxa_id
+      return @ncbi_taxa_id
+    end
 
-      def feature_key(k_id)
-        query = "select * from seqfeature_key where seqfeature_key_id = ?"
-        row = @dbh.execute(query, k_id).fetch
-        row ? row['key_name'] : ''
-      end
 
-      def feature_source(s_id)
-        query = "select * from seqfeature_source where seqfeature_source_id = ?"
-        row = @dbh.execute(query, s_id).fetch
-        row ? row['source_name'] : ''
-      end
+    private
 
-      def feature_locations(f_id)
-        locations = []
-        query = "select * from seqfeature_location where seqfeature_id = ?"
-        @dbh.execute(query, f_id).fetch_all.each do |row|
-          next unless row
+    def feature_key(k_id)
+      query = "select * from term where term_id= ?"
+      row = @dbh.execute(query, k_id).fetch
+      row ? row['name'] : ''
+    end
 
-          location = Bio::Location.new
-          location.strand = row['seq_strand']
-          location.from = row['seq_start']
-          location.to = row['seq_end']
+    def feature_source(s_id)
+      query = "select * from term where term_id = ?"
+      row = @dbh.execute(query, s_id).fetch
+      row ? row['name'] : ''
+    end
 
-          xref = feature_locations_remote(row['seqfeature_location_id'])
-          location.xref_id = xref.shift unless xref.empty?
+    def feature_locations(f_id)
+      locations = []
+      query = "select * from location where seqfeature_id = ?"
+      @dbh.execute(query, f_id).fetch_all.each do |row|
+        next unless row
 
-          # just omit fuzzy location for now...
-          #feature_locations_qv(row['seqfeature_location_id'])
+        location = Bio::Location.new
+        location.strand = row['strand']
+        location.from = row['start_pos']
+        location.to = row['end_pos']
 
-          rank = row['location_rank'].to_i - 1
-          locations[rank] = location
-        end
-        return Bio::Locations.new(locations)
-      end
+        xref = feature_locations_remote(row['dbxref_if'])
+        location.xref_id = xref.shift unless xref.empty?
 
-      def feature_locations_remote(l_id)
-        query = "select * from remote_seqfeature_name where seqfeature_location_id = ?"
-        row = @dbh.execute(query, l_id).fetch
-        row ? [row['accession'], row['version']] : []
-      end
+        # just omit fuzzy location for now...
+        #feature_locations_qv(row['seqfeature_location_id'])
 
-      def feature_locations_qv(l_id)
-        query = "select * from location_qualifier_value where seqfeature_location_id = ?"
-        row = @dbh.execute(query, l_id).fetch
-        row ? [row['qualifier_value'], row['slot_value']] : []
+        rank = row['rank'].to_i - 1
+        locations[rank] = location
       end
+      return Bio::Locations.new(locations)
+    end
 
-      def feature_qualifiers(f_id)
-        qualifiers = []
-        query = "select * from seqfeature_qualifier_value where seqfeature_id = ?"
-        @dbh.execute(query, f_id).fetch_all.each do |row|
-          next unless row
+    def feature_locations_remote(l_id)
+      query = "select * from  dbxref where dbxref_id = ?"
+      row = @dbh.execute(query, l_id).fetch
+      row ? [row['accession'], row['version']] : []
+    end
 
-          key = feature_qualifiers_key(row['seqfeature_qualifier_id'])
-          value = row['qualifier_value']
-          qualifier = Bio::Feature::Qualifier.new(key, value)
+    def feature_locations_qv(l_id)
+      query = "select * from location_qualifier_value where location_id = ?"
+      row = @dbh.execute(query, l_id).fetch
+      row ? [row['value'], row['int_value']] : []
+    end
 
-          rank = row['seqfeature_qualifier_rank'].to_i - 1
-          qualifiers[rank] = qualifier
-        end
-        return qualifiers.compact	# .compact is nasty hack for a while
-      end
+    def feature_qualifiers(f_id)
+      qualifiers = []
+      query = "select * from seqfeature_qualifier_value where seqfeature_id = ?"
+      @dbh.execute(query, f_id).fetch_all.each do |row|
+        next unless row
 
-      def feature_qualifiers_key(q_id)
-        query = "select * from seqfeature_qualifier where seqfeature_qualifier_id = ?"
-        row = @dbh.execute(query, q_id).fetch
-        row ? row['qualifier_name'] : ''
+        key = feature_qualifiers_key(row['seqfeature_id'])
+        value = row['value']
+        qualifier = Bio::Feature::Qualifier.new(key, value)
+
+        rank = row['rank'].to_i - 1
+        qualifiers[rank] = qualifier
       end
+      return qualifiers.compact	# .compact is nasty hack for a while
     end
 
+    def feature_qualifiers_key(q_id)
+      query = <<-END
+        select * from seqfeature_qualifier_value
+        join term using(term_id) where seqfeature_id = ?
+      END
+      row = @dbh.execute(query, q_id).fetch
+      row ? row['name'] : ''
+    end
   end
 
-end
+end # SQL
+
+end # Bio
 
 
 if __FILE__ == $0
@@ -364,65 +363,3 @@ if __FILE__ == $0
 
 end
 
-
-=begin
-
-= Bio::SQL
-
---- Bio::SQL.new(db = 'dbi:Mysql:biosql', user = nil, pass = nil)
-
---- Bio::SQL.close
-
---- Bio::SQL#fetch(accession)
-
-      Returns Bio::SQL::Sequence object.
-
-== Bio::SQL::Sequence
-
---- Bio::SQL::Sequence.new(dbh, entry)
-
---- Bio::SQL::Sequence#accession -> String
---- Bio::SQL::Sequence#comment -> String
-
-      Returns the first comment.  For complete comments, use comments method.
-
---- Bio::SQL::Sequence#comments -> Array
-
-      Returns comments in an Array of Strings.
-
---- Bio::SQL::Sequence#common_name -> String
---- Bio::SQL::Sequence#database -> String
---- Bio::SQL::Sequence#date -> String
---- Bio::SQL::Sequence#dblink -> Array
---- Bio::SQL::Sequence#definition -> String
---- Bio::SQL::Sequence#division -> String
---- Bio::SQL::Sequence#entry_id -> String
-
---- Bio::SQL::Sequence#features
-
-      Returns Bio::Features object.
-
---- Bio::SQL::Sequence#keyword -> String
---- Bio::SQL::Sequence#lineage -> String
---- Bio::SQL::Sequence#ncbi_taxa_id -> String
-
---- Bio::SQL::Sequence#references -> Array
-
-      Returns reference informations in Array of Hash (not Bio::Reference).
-
---- Bio::SQL::Sequence#seq
-
-      Returns Bio::Sequence::NA or AA object.
-
---- Bio::SQL::Sequence#subseq(from, to)
-
-      Returns Bio::Sequence::NA or AA object (by lazy fetching).
-
---- Bio::SQL::Sequence#taxonomy -> DBI::Row
-
-      Use lineage, common_name, ncbi_taxa_id methods to extract in detail.
-
---- Bio::SQL::Sequence#version -> String
-
-=end
-