bio 0.7.1 → 1.0.0

data/lib/bio/appl/emboss.rb

@@ -1,68 +1,61 @@
 #
-# bio/appl/emboss.rb - EMBOSS wrapper
+# = bio/appl/emboss.rb - EMBOSS wrapper
 # 
-#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::	Copyright (C) 2002, 2005
+#		KATAYAMA Toshiaki <k@bioruby.org>
+# License::	Ruby's
 #
-#  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.
+# $Id: emboss.rb,v 1.4 2006/02/27 09:14:30 k Exp $
 #
-#  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.
+# == References
 #
-#  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: emboss.rb,v 1.2 2005/09/08 01:22:08 k Exp $
+# * http://www.emboss.org
 #
 
 module Bio
 
-  class EMBOSS
+autoload :Command, 'bio/command'
 
-    def initialize(cmd_line)
-      @cmd_line = cmd_line + ' -stdout'
-    end
+class EMBOSS
 
-    def exec
-      begin
-        @io = IO.popen(@cmd_line, "w+")
-        @result = @io.read
-        return @result
-      ensure
-        @io.close
-      end
-    end
-    attr_reader :io, :result
+  extend Bio::Command::Tools
 
+  def self.seqret(arg)
+    str = self.retrieve('seqret', arg)
   end
 
-end
-
-=begin
-
-= Bio::EMBOSS
-
-EMBOSS wrapper.
+  def self.entret(arg)
+    str = self.retrieve('entret', arg)
+  end
 
-  #!/usr/bin/env ruby
-  require 'bio'
+  def initialize(cmd_line)
+    @cmd_line = cmd_line + ' -stdout -auto'
+  end
 
-  emboss = Bio::EMBOSS.new("getorf -sequence ~/xlrhodop -outseq stdout")
-  puts emboss.exec
+  def exec
+    begin
+      @io = IO.popen(@cmd_line, "w+")
+      @result = @io.read
+      return @result
+    ensure
+      @io.close
+    end
+  end
+  attr_reader :io, :result
 
---- Bio::EMBOSS.new(command_line)
+  private
 
---- Bio::EMBOSS#exec
---- Bio::EMBOSS#io
---- Bio::EMBOSS#result
+  def self.retrieve(cmd, arg)
+    cmd = [ cmd, arg, '-auto', '-stdout' ]
+    str = ''
+    call_command_local(cmd) do |inn, out|
+      inn.close_write
+      str = out.read
+    end
+    return str
+  end
 
-=== SEE ALSO
+end # EMBOSS
 
-* http://www.emboss.org
+end # Bio
 
-=end

data/lib/bio/appl/hmmer.rb

@@ -1,7 +1,32 @@
 #
-# bio/appl/hmmer.rb - HMMER wrapper
+# = bio/appl/hmmer.rb - HMMER wrapper
 # 
-#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::   Copyright (C) 2002 
+#               KATAYAMA Toshiaki <k@bioruby.org>
+# Lisence::     LGPL
+#
+# $Id: hmmer.rb,v 1.5 2006/02/02 17:08:36 nakao Exp $
+#
+# == Description
+#
+# A wrapper for the HMMER programs (hmmsearch or hmmpfam).
+#
+# == Examples
+#
+#   require 'bio'
+#   program = 'hmmsearch' # or 'hmmpfam'
+#   hmmfile = 'test.hmm'
+#   seqfile = 'test.faa'
+#   
+#   factory = Bio::HMMER.new(program, hmmfile, seqfile)
+#   p factory.query
+#
+# == References
+#
+# * HMMER
+#   http://hmmer.wustl.edu/
+#
+#--
 #
 #  This library is free software; you can redistribute it and/or
 #  modify it under the terms of the GNU Lesser General Public
@@ -17,7 +42,7 @@
 #  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: hmmer.rb,v 1.4 2005/09/26 13:00:04 k Exp $
+#++
 #
 
 require 'bio/command'
@@ -25,105 +50,114 @@ require 'shellwords'
 
 module Bio
 
-  class HMMER
-
-    autoload :Report, 'bio/appl/hmmer/report'
+# A wapper for HMMER programs (hmmsearch or hmmpfam).
+#
+# === Examples
+#
+#   require 'bio'
+#   program = 'hmmsearch' # or 'hmmpfam'
+#   hmmfile = 'test.hmm'
+#   seqfile = 'test.faa'
+#   
+#   factory = Bio::HMMER.new(program, hmmfile, seqfile)
+#   report = factory.query
+#   report.class #=> Bio::HMMER::Report
+#
+# === References
+#
+# * HMMER
+#   http://hmmer.wustl.edu/
+#
+class HMMER
+
+  autoload :Report, 'bio/appl/hmmer/report'
+
+  include Bio::Command::Tools
+
+  # Prgrams name. (hmmsearch or hmmpfam).
+  attr_accessor :program
+  
+  # Name of hmmfile.
+  attr_accessor :hmmfile
+  
+  # Name of seqfile.
+  attr_accessor :seqfile
+  
+  #  Command line options.
+  attr_accessor :options
+  
+  # Shows the raw output from the hmmer search.
+  attr_reader :output
+
+  # Sets a program name, a profile hmm file name, a query sequence file name 
+  # and options in string.
+  # 
+  # Program names: hmmsearch, hmmpfam
+  #
+  def initialize(program, hmmfile, seqfile, options = [])
+    @program = program
+    @hmmfile = hmmfile
+    @seqfile = seqfile
+    @output  = ''
+    
+    begin
+      @options = opt.to_ary
+    rescue NameError #NoMethodError
+      # backward compatibility
+      @options = Shellwords.shellwords(options)
+    end
+  end
 
-    include Bio::Command::Tools
 
-    def initialize(program, hmmfile, seqfile, opt = [])
-      @program	= program
-      @hmmfile	= hmmfile
-      @seqfile	= seqfile
-      @output	= ''
+  # Gets options by String.
+  # backward compatibility.
+  def option
+    make_command_line(@options)
+  end
 
-      begin
-        @options = opt.to_ary
-      rescue NameError #NoMethodError
-        # backward compatibility
-        @options = Shellwords.shellwords(opt)
-      end
-    end
-    attr_accessor :program, :hmmfile, :seqfile, :options
-    attr_reader :output
 
-    def option
-      # backward compatibility
-      make_command_line(@options)
-    end
+  # Sets options by String.
+  # backward compatibility.
+  def option=(str)
+    @options = Shellwords.shellwords(str)
+  end
 
-    def option=(str)
-      # backward compatibility
-      @options = Shellwords.shellwords(str)
-    end
 
-    def query
-      cmd = [ @program, *@options ]
-      cmd.concat([ @hmmfile, @seqfile ])
+  # Executes the hmmer search and returns the report 
+  # (Bio::HMMER::Report object).
+  def query
+    cmd = [ @program, *@options ]
+    cmd.concat([ @hmmfile, @seqfile ])
       
-      report = nil
-
-      @output = call_command_local(cmd, nil)
-      report = parse_result(@output)
+    report = nil
+    
+    @output = call_command_local(cmd, nil)
+    report = parse_result(@output)
       
-      return report
-    end
-
+    return report
+  end
 
-    private
+  private
+  
+  def parse_result(data)
+    Report.new(data)
+  end
 
-    def parse_result(data)
-      Report.new(data)
-    end
+end # class HMMER
 
-  end
-end
+end # module Bio
 
 
 
 if __FILE__ == $0
 
-  begin
-    require 'pp'
-    alias p pp
-  rescue
-  end
+  require 'pp'
 
-  program = ARGV.shift	# hmmsearch, hmmpfam
+  program = ARGV.shift # hmmsearch, hmmpfam
   hmmfile = ARGV.shift
   seqfile = ARGV.shift
 
   factory = Bio::HMMER.new(program, hmmfile, seqfile)
-  p factory.query
+  pp factory.query
 
 end
-
-
-=begin
-
-= Bio::HMMER
-
---- Bio::HMMER.new(program, hmmfile, seqfile, option = '')
---- Bio::HMMER#program
---- Bio::HMMER#hmmfile
---- Bio::HMMER#seqfile
---- Bio::HMMER#options
-
-      Accessors for the factory.
-
---- Bio::HMMER#option
---- Bio::HMMER#option=(str)
-
-      Get/set options by string.
-
---- Bio::HMMER#query
-
-      Executes the hmmer search and returns Report object (Bio::HMMER::Report).
-
---- Bio::HMMER#output
-
-      Shows the raw output from hmmer search.
-
-=end
-
-

data/lib/bio/appl/hmmer/report.rb

@@ -1,8 +1,44 @@
 #
-# bio/appl/hmmer/report.rb - hmmsearch, hmmpfam parserer
+# = bio/appl/hmmer/report.rb - hmmsearch, hmmpfam parserer
 #
-#   Copyright (C) 2002 Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>
-#   Copyright (C) 2005 Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>
+# Copyright::   Copyright (C) 2002 
+#               Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>,
+# Copyright::   Copyright (C) 2005 
+#               Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>
+# Lisence::     LGPL
+#
+# $Id: report.rb,v 1.10 2006/02/02 17:08:36 nakao Exp $
+#
+# == Description
+#
+# Parser class for hmmsearch and hmmpfam in the HMMER package.
+#
+# == Examples
+#
+#    #for multiple reports in a single output file (example.hmmpfam)
+#    Bio::HMMER.reports(File.read("example.hmmpfam")) do |report|
+#      report.program['name']
+#      report.parameter['HMM file']
+#      report.query_info['Query sequence']
+#      report.hits.each do |hit|
+#        hit.accession
+#        hit.description
+#        hit.score
+#        hit.evalue
+#        hit.hsps.each do |hsp|
+#          hsp.accession
+#          hsp.domain
+#          hsp.evalue
+#          hsp.midline
+#      end
+#    end
+#
+# == References
+#
+# * HMMER
+#   http://hmmer.wustl.edu/
+#
+#--
 #
 #  This library is free software; you can redistribute it and/or
 #  modify it under the terms of the GNU Lesser General Public
@@ -18,340 +54,534 @@
 #  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: report.rb,v 1.9 2005/10/31 09:12:03 k Exp $
+#++
 #
 
 require 'bio/appl/hmmer'
 
 module Bio
-  class HMMER
 
-    def self.reports(input)
-      ary = []
-      input.each("\n//\n") do |data|
-        if block_given?
-          yield Report.new(data)
-        else
-          ary << Report.new(data)
-        end
+
+class HMMER
+
+  # A reader interface for multiple reports text into a report 
+  # (Bio::HMMER::Report).
+  #
+  # === Examples
+  # 
+  #   # Iterator
+  #   Bio::HMMER.reports(reports_text) do |report|
+  #     report
+  #   end
+  #
+  #   # Array
+  #   reports = Bio::HMMER.reports(reports_text)
+  #
+  def self.reports(multiple_report_text)
+    ary = []
+    multiple_report_text.each("\n//\n") do |report|
+      if block_given?
+        yield Report.new(report)
+      else
+        ary << Report.new(report)
       end
-      return ary
     end
+    return ary
+  end
 
 
-    # Bio::HMMER::Report
-    class Report
-
-      # for Bio::FlatFile support
-      DELIMITER = RS = "\n//\n"
+  # A parser class for a search report by hmmsearch or hmmpfam program in the 
+  # HMMER package. 
+  #
+  # === Examples
+  # 
+  #   Examples
+  #    #for multiple reports in a single output file (example.hmmpfam)
+  #    Bio::HMMER.reports(File.read("example.hmmpfam")) do |report|
+  #      report.program['name']
+  #      report.parameter['HMM file']
+  #      report.query_info['Query sequence']
+  #      report.hits.each do |hit|
+  #        hit.accession
+  #        hit.description
+  #        hit.score
+  #        hit.evalue
+  #        hit.hsps.each do |hsp|
+  #          hsp.accession
+  #          hsp.domain
+  #          hsp.evalue
+  #          hsp.midline
+  #      end
+  #    end
+  #
+  # === References
+  #
+  # * HMMER 
+  #   http://hmmer.wustl.edu/
+  #
+  class Report
+    
+    # Delimiter of each entry for Bio::FlatFile support.
+    DELIMITER = RS = "\n//\n"
+
+    
+    # A Hash contains program information used. 
+    # Valid keys are 'name', 'version', 'copyright' and 'license'.
+    attr_reader :program
+
+    # A hash contains parameters used.
+    # Valid keys are 'HMM file' and 'Sequence file'.
+    attr_reader :parameter
+    
+    # A hash contains the query information.
+    # Valid keys are 'query sequence', 'Accession' and 'Description'.
+    attr_reader :query_info
+
+    # 
+    attr_reader :hits
+    
+    # Returns an Array of Bio::HMMER::Report::Hsp objects.
+    # Under special circumstances, some HSPs do not have
+    # parent Hit objects. If you want to access such HSPs,
+    # use this method.
+    attr_reader :hsps
+
+    # statistics by hmmsearch.
+    attr_reader :histogram
+    
+    # statistics by hmmsearch. Keys are 'mu', 'lambda', 'chi-sq statistic' and 'P(chi-square)'.
+    attr_reader :statistical_detail
+    
+    # statistics by hmmsearch.
+    attr_reader :total_seq_searched
+    
+    # statistics by hmmsearch. Keys are 'Total memory', 'Satisfying E cutoff' and 'Total hits'. 
+    attr_reader :whole_seq_top_hits
+    
+    # statistics by hmmsearch. Keys are 'Total memory', 'Satisfying E cutoff' and 'Total hits'. 
+    attr_reader :domain_top_hits
+
+
+    # Parses a HMMER search report (by hmmpfam or hmmsearch program) and 
+    # reutrns a Bio::HMMER::Report object.
+    # 
+    # === Examples
+    #
+    #   hmmpfam_report = Bio::HMMER::Report.new(File.read("hmmpfam.out"))
+    #   
+    #   hmmsearch_report = Bio::HMMER::Report.new(File.read("hmmsearch.out"))
+    #
+    def initialize(data)
+
+      # The input data is divided into six data fields, i.e. header,
+      # query infomation, hits, HSPs, alignments and search statistics.
+      # However, header and statistics data don't necessarily exist.
+      subdata, is_hmmsearch = get_subdata(data)
+
+      # if header exists, parse it
+      if subdata["header"]
+        @program, @parameter = parse_header_data(subdata["header"])
+      else
+        @program, @parameter = [{}, {}]
+      end
 
-      def initialize(data)
+      @query_info = parse_query_info(subdata["query"])
+      @hits       = parse_hit_data(subdata["hit"])
+      @hsps       = parse_hsp_data(subdata["hsp"], is_hmmsearch)
 
-        # The input data is divided into six data fields, i.e. header,
-        # query infomation, hits, HSPs, alignments and search statistics.
-        # However, header and statistics data don't necessarily exist.
-        subdata, is_hmmsearch = get_subdata(data)
+      if @hsps != []
+        # split alignment subdata into an array of alignments
+        aln_ary = subdata["alignment"].split(/^\S+.*?\n/).slice(1..-1)
 
-        # if header exists, parse it
-        if subdata["header"]
-          @program, @parameter = parse_header_data(subdata["header"])
-        else
-          @program, @parameter = [{}, {}]
+        # append alignment information to corresponding Hsp
+        aln_ary.each_with_index do |aln, i|
+          @hsps[i].set_alignment(aln)
         end
+      end
 
-        @query_info = parse_query_info(subdata["query"])
-        @hits       = parse_hit_data(subdata["hit"])
-        @hsps       = parse_hsp_data(subdata["hsp"], is_hmmsearch)
-
-        if @hsps != []
-          # split alignment subdata into an array of alignments
-          aln_ary = subdata["alignment"].split(/^\S+.*?\n/).slice(1..-1)
-
-          # append alignment information to corresponding Hsp
-          aln_ary.each_with_index do |aln, i|
-            @hsps[i].set_alignment(aln)
-          end
+      # assign each Hsp object to its parent Hit
+      hits_hash = {}
+      @hits.each do |hit|
+        hits_hash[hit.accession] = hit
+      end
+      @hsps.each do |hsp|
+        if hits_hash.has_key?(hsp.accession)
+          hits_hash[hsp.accession].append_hsp(hsp)
         end
+      end
 
-        # assign each Hsp object to its parent Hit
-        hits_hash = {}
-        @hits.each do |hit|
-          hits_hash[hit.accession] = hit
-        end
-        @hsps.each do |hsp|
-          if hits_hash.has_key?(hsp.accession)
-            hits_hash[hsp.accession].append_hsp(hsp)
-          end
-        end
+      # parse statistics (for hmmsearch)
+      if is_hmmsearch
+        @histogram, @statistical_detail, @total_seq_searched, \
+        @whole_seq_top_hits, @domain_top_hits = \
+        parse_stat_data(subdata["statistics"])
+      end
+
+    end
 
-        # parse statistics (for hmmsearch)
-        if is_hmmsearch
-          @histogram, @statistical_detail, @total_seq_searched, \
-          @whole_seq_top_hits, @domain_top_hits = \
-          parse_stat_data(subdata["statistics"])
-        end
 
+    # Iterates each hit (Bio::HMMER::Report::Hit).
+    def each
+      @hits.each do |hit|
+        yield hit
+      end
+    end
+    alias :each_hit :each
+
+
+    # Bio::HMMER::Report#get_subdata
+    def get_subdata(data)
+      subdata = {}
+      header_prefix = '\Ahmm(search|pfam) - search'
+      query_prefix  = '^Query (HMM|sequence): .*\nAccession: '
+      hit_prefix    = '^Scores for (complete sequences|sequence family)'
+      hsp_prefix    = '^Parsed for domains:'
+      aln_prefix    = '^Alignments of top-scoring domains:\n'
+      stat_prefix   = '^\nHistogram of all scores:'
+
+      # if header exists, get it
+      if data =~ /#{header_prefix}/
+        is_hmmsearch = ($1 == "search")   # hmmsearch or hmmpfam
+        subdata["header"] = data[/(\A.+?)(?=#{query_prefix})/m]
+      else
+        is_hmmsearch = false   # if no header, assumed to be hmmpfam
       end
-      attr_reader :program, :parameter, :query_info, :hits, :hsps,
-        :histogram, :statistical_detail, :total_seq_searched,
-        :whole_seq_top_hits, :domain_top_hits
 
+      # get query, Hit and Hsp data
+      subdata["query"] = data[/(#{query_prefix}.+?)(?=#{hit_prefix})/m]
+      subdata["hit"]   = data[/(#{hit_prefix}.+?)(?=#{hsp_prefix})/m]
+      subdata["hsp"]   = data[/(#{hsp_prefix}.+?)(?=#{aln_prefix})/m]
+
+      # get alignment data
+      if is_hmmsearch
+        data =~ /#{aln_prefix}(.+?)#{stat_prefix}/m
+        subdata["alignment"] = $1
+      else
+        data =~ /#{aln_prefix}(.+?)\/\/\n/m
+        subdata["alignment"] = $1
+        raise "multiple reports found" if $'.length > 0
+      end
+      
+      # handle -A option of HMMER
+      cutoff_line = '\t\[output cut off at A = \d+ top alignments\]\n\z'
+      subdata["alignment"].sub!(/#{cutoff_line}/, '')
+      
+      # get statistics data
+      subdata["statistics"] = data[/(#{stat_prefix}.+)\z/m]
 
-      def each
-        @hits.each do |x|
-          yield x
+      [subdata, is_hmmsearch]
+    end
+    private :get_subdata
+    
+  
+    # Bio::HMMER::Report#parse_header_data
+    def parse_header_data(data)
+      data =~ /\A(.+? - - -$\n)(.+? - - -$\n)\n\z/m
+      program_data   = $1
+      parameter_data = $2
+      
+      program = {}
+      program['name'], program['version'], program['copyright'], \
+      program['license'] = program_data.split(/\n/)
+      
+      parameter = {}
+      parameter_data.each do |x|
+        if /^(.+?):\s+(.*?)\s*$/ =~ x
+          parameter[$1] = $2
         end
       end
 
+      [program, parameter]
+    end
+    private :parse_header_data
 
-      # Bio::HMMER::Report::Hit
-      class Hit
-        def initialize(data)
-          @hsps = Array.new
-          if /^(\S+)\s+(.*?)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ data
-            @accession, @description, @score, @evalue, @num = 
-              [$1, $2, $3.to_f, $4.to_f, $5.to_i]
-          end
-        end
-        attr_reader :hsps, :accession, :description, :score, :evalue, :num
 
-        def each
-          @hsps.each do |x|
-            yield x
-          end
+    # Bio::HMMER::Report#parse_query_info
+    def parse_query_info(data)
+      hash = {}
+      data.each do |x|
+        if /^(.+?):\s+(.*?)\s*$/ =~ x
+          hash[$1] = $2
+        elsif /\s+\[(.+)\]/ =~ x
+          hash['comments'] = $1
         end
-
-        alias target_id  accession
-        alias hit_id     accession
-        alias entry_id   accession
-        alias definition description
-        alias bit_score  score
-
-        def target_def
-          if @hsps.size == 1
-            "<#{@hsps[0].domain}> #{@description}"
-          else
-            "<#{@num.to_s}> #{@description}"
-          end
+      end
+      hash
+    end
+    private :parse_query_info
+
+    
+    # Bio::HMMER::Report#parse_hit_data
+    def parse_hit_data(data)
+      data.sub!(/.+?---\n/m, '').chop!
+      hits = []
+      return hits if data == "\t[no hits above thresholds]\n"
+      data.each do |l|
+        hits.push(Hit.new(l))
+      end
+      hits
+    end
+    private :parse_hit_data
+
+    
+    # Bio::HMMER::Report#parse_hsp_data
+    def parse_hsp_data(data, is_hmmsearch)
+      data.sub!(/.+?---\n/m, '').chop!
+      hsps=[]
+      return hsps if data == "\t[no hits above thresholds]\n"
+      data.each do |l|
+        hsps.push(Hsp.new(l, is_hmmsearch))
+      end
+      return hsps
+    end
+    private :parse_hsp_data
+
+    
+    # Bio::HMMER::Report#parse_stat_data
+    def parse_stat_data(data)
+      data.sub!(/\nHistogram of all scores:\n(.+?)\n\n\n%/m, '')
+      histogram = $1.strip
+
+      statistical_detail = {}
+      data.sub!(/(.+?)\n\n/m, '')
+      $1.each do |l|
+        statistical_detail[$1] = $2.to_f if /^\s*(.+?)\s*=\s*(\S+)/ =~ l
+      end
+        
+      total_seq_searched = nil
+      data.sub!(/(.+?)\n\n/m, '')
+      $1.each do |l|
+        total_seq_searched = $2.to_i if /^\s*(.+)\s*:\s*(\S+)/ =~ l
+      end
+        
+      whole_seq_top_hits = {}
+      data.sub!(/(.+?)\n\n/m, '')
+      $1.each do |l|
+        if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
+          whole_seq_top_hits[$1] = $2.to_i
+        elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
+          whole_seq_top_hits[$1] = $2
         end
-
-        def append_hsp(hsp)
-          @hsps << hsp
+      end
+        
+      domain_top_hits = {}
+      data.each do |l|
+        if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
+          domain_top_hits[$1] = $2.to_i
+        elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
+          domain_top_hits[$1] = $2
         end
-
       end
 
+      [histogram, statistical_detail, total_seq_searched, \
+        whole_seq_top_hits, domain_top_hits]
+    end
+    private :parse_stat_data
 
-      # Bio::HMMER::Report::Hsp
-      class Hsp
-        def initialize(data, is_hmmsearch)
-          @is_hmmsearch = is_hmmsearch
-
-          @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
-            score, evalue = data.split(' ')
-          @seq_f = seq_f.to_i
-          @seq_t = seq_t.to_i
-          @hmm_f = hmm_f.to_i
-          @hmm_t = hmm_t.to_i
-          @score = score.to_f
-          @evalue = evalue.to_f
-          @hmmseq = ''
-          @flatseq = ''
-          @midline = ''
-          @query_frame = 1
-          @target_frame = 1
-          # CS and RF lines are rarely used.
-          @csline = nil
-          @rfline = nil
-        end
-        attr_reader :accession, :domain, :seq_f, :seq_t, :seq_ft,
-          :hmm_f, :hmm_t, :hmm_ft, :score, :evalue, :midline, :hmmseq,
-          :flatseq, :query_frame, :target_frame, :csline, :rfline
-
-        def set_alignment(aln)
-          # First, split the input alignment into an array of
-          # "alignment blocks." One block usually has three lines,
-          # i.e. hmmseq, midline and flatseq. 
-          # However, although infrequent, it can contain CS or RF lines.
-          aln.split(/ (?:\d+|-)\s*\n\n/).each do |blk|
-            lines = blk.split(/\n/)   
-            cstmp = (lines[0] =~ /^ {16}CS/) ? lines.shift : nil
-            rftmp = (lines[0] =~ /^ {16}RF/) ? lines.shift : nil
-            aln_width = lines[0][/\S+/].length
-            @csline  = @csline.to_s + cstmp[19, aln_width] if cstmp
-            @rfline  = @rfline.to_s + rftmp[19, aln_width] if rftmp
-            @hmmseq  += lines[0][19, aln_width]
-            @midline += lines[1][19, aln_width]
-            @flatseq += lines[2][19, aln_width]
-          end
-          @csline  = @csline[3...-3] if @csline
-          @rfline  = @rfline[3...-3] if @rfline
-          @hmmseq  = @hmmseq[3...-3]
-          @midline = @midline[3...-3]
-          @flatseq = @flatseq[3...-3]
-        end
 
-        def query_seq;   @is_hmmsearch ? @hmmseq  : @flatseq; end
-        def target_seq;  @is_hmmsearch ? @flatseq : @hmmseq;  end
-        def target_from; @is_hmmsearch ? @seq_f   : @hmm_f;   end
-        def target_to;   @is_hmmsearch ? @seq_t   : @hmm_t;   end
-        def query_from;  @is_hmmsearch ? @hmm_f   : @seq_f;   end
-        def query_to;    @is_hmmsearch ? @hmm_t   : @seq_t;   end
+    # Container class for HMMER search hits.
+    class Hit
+
+      # An Array of Bio::HMMER::Report::Hsp objects. 
+      attr_reader :hsps
 
-        alias bit_score score
-        alias target_id accession
+      # 
+      attr_reader :accession
+      alias target_id  accession
+      alias hit_id     accession
+      alias entry_id   accession
+      
+      # 
+      attr_reader :description
+      alias definition description
+
+      # Matching scores (total of all HSPs).
+      attr_reader :score
+      alias bit_score score 
+
+      # E-value
+      attr_reader :evalue
 
+      # Number of domains
+      attr_reader :num
+        
+      # Sets hit data.
+      def initialize(hit_data)
+        @hsps = Array.new
+        if /^(\S+)\s+(.*?)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ hit_data
+          @accession, @description, @score, @evalue, @num = \
+          [$1, $2, $3.to_f, $4.to_f, $5.to_i]
+        end
       end
 
 
-      # Bio::HMMER::Report#get_subdata
-      def get_subdata(data)
-        subdata = {}
-        header_prefix = '\Ahmm(search|pfam) - search'
-        query_prefix  = '^Query (HMM|sequence): .*\nAccession: '
-        hit_prefix    = '^Scores for (complete sequences|sequence family)'
-        hsp_prefix    = '^Parsed for domains:'
-        aln_prefix    = '^Alignments of top-scoring domains:\n'
-        stat_prefix   = '^\nHistogram of all scores:'
-
-        # if header exists, get it
-        if data =~ /#{header_prefix}/
-          is_hmmsearch = ($1 == "search")   # hmmsearch or hmmpfam
-          subdata["header"] = data[/(\A.+?)(?=#{query_prefix})/m]
-        else
-          is_hmmsearch = false   # if no header, assumed to be hmmpfam
+      # Iterates on each Hsp object (Bio::HMMER::Report::Hsp).
+      def each
+        @hsps.each do |hsp|
+          yield hsp
         end
+      end
+      alias :each_hsp :each
 
-        # get query, Hit and Hsp data
-        subdata["query"] = data[/(#{query_prefix}.+?)(?=#{hit_prefix})/m]
-        subdata["hit"]   = data[/(#{hit_prefix}.+?)(?=#{hsp_prefix})/m]
-        subdata["hsp"]   = data[/(#{hsp_prefix}.+?)(?=#{aln_prefix})/m]
 
-        # get alignment data
-        if is_hmmsearch
-          data =~ /#{aln_prefix}(.+?)#{stat_prefix}/m
-          subdata["alignment"] = $1
+      # Shows the hit description.
+      def target_def
+        if @hsps.size == 1
+          "<#{@hsps[0].domain}> #{@description}"
         else
-          data =~ /#{aln_prefix}(.+?)\/\/\n/m
-          subdata["alignment"] = $1
-          raise "multiple reports found" if $'.length > 0
+          "<#{@num.to_s}> #{@description}"
         end
+      end
 
-        # handle -A option of HMMER
-        cutoff_line = '\t\[output cut off at A = \d+ top alignments\]\n\z'
-        subdata["alignment"].sub!(/#{cutoff_line}/, '')
+      # Appends a Bio::HMMER::Report::Hsp object.
+      def append_hsp(hsp)
+        @hsps << hsp
+      end
+      
+    end # class Hit
 
-        # get statistics data
-        subdata["statistics"] = data[/(#{stat_prefix}.+)\z/m]
 
-        [subdata, is_hmmsearch]
-      end
-      private :get_subdata
+    # Container class for HMMER search hsps.
+    class Hsp
       
-      # Bio::HMMER::Report#parse_header_data
-      def parse_header_data(data)
-        data =~ /\A(.+? - - -$\n)(.+? - - -$\n)\n\z/m
-        program_data   = $1
-        parameter_data = $2
-
-        program = {}
-        program['name'], program['version'], program['copyright'], \
-        program['license'] = program_data.split(/\n/)
-
-        parameter = {}
-        parameter_data.each do |x|
-          if /^(.+?):\s+(.*?)\s*$/ =~ x
-            parameter[$1] = $2
-          end
-        end
+      # 
+      attr_reader :accession
+      alias target_id accession
+
+      #
+      attr_reader :domain
+      
+      #
+      attr_reader :seq_f
+
+      #
+      attr_reader :seq_t
+
+      #
+      attr_reader :seq_ft
+
+      #
+      attr_reader :hmm_f
+
+      #
+      attr_reader :hmm_t
+
+      #
+      attr_reader :hmm_ft
+
+      # Score
+      attr_reader :score
+      alias bit_score score
+
+      # E-value
+      attr_reader :evalue
+      
+      # Alignment midline
+      attr_reader :midline
+      
+      #
+      attr_reader :hmmseq
+
+      #
+      attr_reader :flatseq
+
+      #
+      attr_reader :query_frame
+
+      #
+      attr_reader :target_frame
 
-        [program, parameter]
+      # CS Line
+      attr_reader :csline
+        
+      # RF Line
+      attr_reader :rfline
+
+      # Sets hsps.
+      def initialize(hsp_data, is_hmmsearch)
+        @is_hmmsearch = is_hmmsearch
+
+        @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,\
+        score, evalue = hsp_data.split(' ')
+        @seq_f = seq_f.to_i
+        @seq_t = seq_t.to_i
+        @hmm_f = hmm_f.to_i
+        @hmm_t = hmm_t.to_i
+        @score = score.to_f
+        @evalue = evalue.to_f
+        @hmmseq = ''
+        @flatseq = ''
+        @midline = ''
+        @query_frame = 1
+        @target_frame = 1
+        # CS and RF lines are rarely used.
+        @csline = nil
+        @rfline = nil
       end
-      private :parse_header_data
-
-      # Bio::HMMER::Report#parse_query_info
-      def parse_query_info(data)
-        hash = {}
-        data.each do |x|
-          if /^(.+?):\s+(.*?)\s*$/ =~ x
-            hash[$1] = $2
-          elsif /\s+\[(.+)\]/ =~ x
-            hash['comments'] = $1
-          end
+
+      #
+      def set_alignment(alignment)
+        # First, split the input alignment into an array of
+        # "alignment blocks." One block usually has three lines,
+        # i.e. hmmseq, midline and flatseq. 
+        # However, although infrequent, it can contain CS or RF lines.
+        alignment.split(/ (?:\d+|-)\s*\n\n/).each do |blk|
+          lines = blk.split(/\n/)   
+          cstmp = (lines[0] =~ /^ {16}CS/) ? lines.shift : nil
+          rftmp = (lines[0] =~ /^ {16}RF/) ? lines.shift : nil
+          aln_width = lines[0][/\S+/].length
+          @csline  = @csline.to_s + cstmp[19, aln_width] if cstmp
+          @rfline  = @rfline.to_s + rftmp[19, aln_width] if rftmp
+          @hmmseq  += lines[0][19, aln_width]
+          @midline += lines[1][19, aln_width]
+          @flatseq += lines[2][19, aln_width]
         end
-        hash
+        @csline  = @csline[3...-3] if @csline
+        @rfline  = @rfline[3...-3] if @rfline
+        @hmmseq  = @hmmseq[3...-3]
+        @midline = @midline[3...-3]
+        @flatseq = @flatseq[3...-3]
       end
-      private :parse_query_info
-
-      # Bio::HMMER::Report#parse_hit_data
-      def parse_hit_data(data)
-        data.sub!(/.+?---\n/m, '').chop!
-        hits = []
-        return hits if data == "\t[no hits above thresholds]\n"
-        data.each do |l|
-          hits.push(Hit.new(l))
-        end
-        hits
+
+
+      #
+      def query_seq
+        @is_hmmsearch ? @hmmseq  : @flatseq
       end
-      private :parse_hit_data
-
-      # Bio::HMMER::Report#parse_hsp_data
-      def parse_hsp_data(data, is_hmmsearch)
-        data.sub!(/.+?---\n/m, '').chop!
-        hsps=[]
-        return hsps if data == "\t[no hits above thresholds]\n"
-        data.each do |l|
-          hsps.push(Hsp.new(l, is_hmmsearch))
-        end
-        return hsps
+
+      #
+      def target_seq
+        @is_hmmsearch ? @flatseq : @hmmseq
+      end
+      
+      #
+      def target_from
+        @is_hmmsearch ? @seq_f   : @hmm_f
       end
-      private :parse_hsp_data
 
-      # Bio::HMMER::Report#parse_stat_data
-      def parse_stat_data(data)
-        data.sub!(/\nHistogram of all scores:\n(.+?)\n\n\n%/m, '')
-        histogram = $1
+      #
+      def target_to
+        @is_hmmsearch ? @seq_t   : @hmm_t
+      end
 
-        statistical_detail = {}
-        data.sub!(/(.+?)\n\n/m, '')
-        $1.each do |l|
-          statistical_detail[$1] = $2.to_f if /^\s*(.+?)\s*=\s*(\S+)/ =~ l
-        end
-        
-        total_seq_searched = nil
-        data.sub!(/(.+?)\n\n/m, '')
-        $1.each do |l|
-          total_seq_searched = $2.to_i if /^\s*(.+)\s*:\s*(\S+)/ =~ l
-        end
-        
-        whole_seq_top_hits = {}
-        data.sub!(/(.+?)\n\n/m, '')
-        $1.each do |l|
-          if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
-            whole_seq_top_hits[$1] = $2.to_i
-          elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
-            whole_seq_top_hits[$1] = $2
-          end
-        end
-        
-        domain_top_hits = {}
-        data.each do |l|
-          if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
-            domain_top_hits[$1] = $2.to_i
-          elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
-            domain_top_hits[$1] = $2
-          end
-        end
+      #
+      def query_from
+        @is_hmmsearch ? @hmm_f   : @seq_f
+      end
 
-        [histogram, statistical_detail, total_seq_searched, \
-          whole_seq_top_hits, domain_top_hits]
+      #
+      def query_to
+        @is_hmmsearch ? @hmm_t   : @seq_t
       end
-      private :parse_stat_data
+      
 
-    end
+    end # class Hsp
 
-  end
-end
+  end # class Report
+
+end # class HMMER
+
+end # module Bio
 
 
 if __FILE__ == $0
@@ -463,94 +693,9 @@ if __FILE__ == $0
       p hsp.query_from		# hmm_f, seq_f
       print "query_to : ".rjust(indent)
       p hsp.query_to		# hmm_t, seq_t
-    end
+    end 
   end
 
-end
-
-
-=begin
-
-= Bio::HMMER::Report
-
---- Bio::HMMER::Report.new(data)
---- Bio::HMMER::Report#each
-
-      Iterates on each Bio::HMMER::Report::Hit object.
-
---- Bio::HMMER::Report#hits
-
-      Returns an Array of Bio::HMMER::Report::Hit objects.
-
-
-== Bio::HMMER::Report::Hit
-
---- Bio::HMMER::Report::Hit#each
-
-      Iterates on each Hsp object.
+end 
 
---- Bio::HMMER::Report::Hit#hsps
-
-      Returns an Array of Bio::HMMER::Report::Hsp objects.
-
---- Bio::HMMER::Report::Hit#target_id
---- Bio::HMMER::Report::Hit#hit_id
---- Bio::HMMER::Report::Hit#entry_id
---- Bio::HMMER::Report::Hit#definition
---- Bio::HMMER::Report::Hit#description
---- Bio::HMMER::Report::Hit#num
-
-      nunmer of domains
-
---- Bio::HMMER::Report::Hit#target_def
-
-      <domain number> + @description
-
---- Bio::HMMER::Report::Hit#evalue
---- Bio::HMMER::Report::Hit#bit_score
---- Bio::HMMER::Report::Hit#score
-
-      Matching scores (total of all HSPs).
-
-
-== Bio::HMMER::Report::Hsp
-
---- Bio::HMMER::Report#hsps
-
-      Returns an Array of Bio::HMMER::Report::Hsp objects.
-      Under special circumstances, some HSPs do not have
-      parent Hit objects. If you want to access such HSPs,
-      use this method.
-
---- Bio::HMMER::Report::Hsp#target_id
---- Bio::HMMER::Report::Hsp#accession
---- Bio::HMMER::Report::Hsp#domain
---- Bio::HMMER::Report::Hsp#seq_f
---- Bio::HMMER::Report::Hsp#seq_t
---- Bio::HMMER::Report::Hsp#seq_ft
---- Bio::HMMER::Report::Hsp#hmm_f
---- Bio::HMMER::Report::Hsp#hmm_t
---- Bio::HMMER::Report::Hsp#hmm_ft
-
---- Bio::HMMER::Report::Hsp#bit_score
---- Bio::HMMER::Report::Hsp#score
---- Bio::HMMER::Report::Hsp#evalue
-
---- Bio::HMMER::Report::Hsp#midline
---- Bio::HMMER::Report::Hsp#hmmseq
---- Bio::HMMER::Report::Hsp#flatseq
---- Bio::HMMER::Report::Hsp#query_frame
---- Bio::HMMER::Report::Hsp#target_frame
-
---- Bio::HMMER::Report::Hsp#query_seq
---- Bio::HMMER::Report::Hsp#query_from
---- Bio::HMMER::Report::Hsp#query_to
---- Bio::HMMER::Report::Hsp#target_seq
---- Bio::HMMER::Report::Hsp#target_from
---- Bio::HMMER::Report::Hsp#target_to
-
---- Bio::HMMER::Report::Hsp#csline
---- Bio::HMMER::Report::Hsp#rfline
-
-=end