bio 1.0.0 → 1.1.0

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

@@ -1,23 +1,10 @@
 #
-# bio/appl/blast/report.rb - BLAST Report class
+# = bio/appl/blast/report.rb - BLAST Report class
 # 
-#   Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2003 Toshiaki Katayama <k@bioruby.org>
+# 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: report.rb,v 1.9 2005/09/26 13:00:04 k Exp $
+# $Id: report.rb,v 1.11 2007/04/05 23:35:39 trevor Exp $
 #
 
 require 'bio/appl/blast'
@@ -26,182 +13,320 @@ require 'bio/appl/blast/rexml'
 require 'bio/appl/blast/format8'
 
 module Bio
-  class Blast
-
-    class Report
+class Blast
 
-      # for Bio::FlatFile support (only for XML data)
-      DELIMITER = RS = "</BlastOutput>\n"
+# = Bio::Blast::Report
+# 
+# Parsed results of the blast execution for Tab-delimited and XML output
+# format.  Tab-delimited reports are consists of
+# 
+#   Query id,
+#   Subject id,
+#   percent of identity,
+#   alignment length,
+#   number of mismatches (not including gaps),
+#   number of gap openings,
+#   start of alignment in query,
+#   end of alignment in query,
+#   start of alignment in subject,
+#   end of alignment in subject,
+#   expected value,
+#   bit score.
+# 
+# according to the MEGABLAST document (README.mbl).  As for XML output,
+# see the following DTDs.
+# 
+#   * http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
+#   * http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod
+#   * http://www.ncbi.nlm.nih.gov/dtd/NCBI_Entity.mod
+# 
+class Report
 
-      def self.xmlparser(data)
-        self.new(data, :xmlparser)
-      end
-      def self.rexml(data)
-        self.new(data, :rexml)
-      end
-      def self.tab(data)
-        self.new(data, :tab)
-      end
+  # for Bio::FlatFile support (only for XML data)
+  DELIMITER = RS = "</BlastOutput>\n"
 
-      def auto_parse(data)
-        if /<?xml/.match(data[/.*/])
-          if defined?(XMLParser)
-            xmlparser_parse(data)
-          else
-            rexml_parse(data)
-          end
-        else
-          tab_parse(data)
-        end
-      end
-      private :auto_parse
-
-      def initialize(data, parser = nil)
-        @iterations = []
-        @parameters = {}
-        case parser
-        when :xmlparser		# format 7
-          xmlparser_parse(data)
-        when :rexml		# format 7
-          rexml_parse(data)
-        when :tab		# format 8
-          tab_parse(data)
-        else
-          auto_parse(data)
-        end
-      end
-      attr_reader :iterations, :parameters,
-        :program, :version, :reference,	:db, :query_id, :query_def, :query_len
-
-      # shortcut for @parameters
-      def matrix;	@parameters['matrix'];			end
-      def expect;	@parameters['expect'].to_i;		end
-      def inclusion;	@parameters['include'].to_i;		end
-      def sc_match;	@parameters['sc-match'].to_i;		end
-      def sc_mismatch;	@parameters['sc-mismatch'].to_i;	end
-      def gap_open;	@parameters['gap-open'].to_i;		end
-      def gap_extend;	@parameters['gap-extend'].to_i;		end
-      def filter;	@parameters['filter'];			end
-      def pattern;	@parameters['pattern'];			end
-      def entrez_query; @parameters['entrez-query'];		end
-
-      # <for blastpgp>
-      def each_iteration
-        @iterations.each do |x|
-          yield x
-        end
-      end
+  # Specify to use XMLParser to parse XML (-m 7) output.
+  def self.xmlparser(data)
+    self.new(data, :xmlparser)
+  end
 
-      # <for blastall> shortcut for the last iteration's hits
-      def each_hit
-        @iterations.last.each do |x|
-          yield x
-        end
-      end
-      alias each each_hit
+  # Specify to use REXML to parse XML (-m 7) output.
+  def self.rexml(data)
+    self.new(data, :rexml)
+  end
 
-      # shortcut for the last iteration's hits
-      def hits
-        @iterations.last.hits
-      end
+  # Specify to use tab delimited output parser.
+  def self.tab(data)
+    self.new(data, :tab)
+  end
 
-      # shortcut for the last iteration's statistics
-      def statistics
-        @iterations.last.statistics
-      end
-      def db_num;	statistics['db-num'];			end
-      def db_len;	statistics['db-len'];			end
-      def hsp_len;	statistics['hsp-len'];			end
-      def eff_space;	statistics['eff-space'];		end
-      def kappa;	statistics['kappa'];			end
-      def lambda;	statistics['lambda'];			end
-      def entropy;	statistics['entropy'];			end
-
-      # shortcut for the last iteration's message (for checking 'CONVERGED')
-      def message
-        @iterations.last.message
+  def auto_parse(data)
+    if /<?xml/.match(data[/.*/])
+      if defined?(XMLParser)
+        xmlparser_parse(data)
+      else
+        rexml_parse(data)
       end
+    else
+      tab_parse(data)
+    end
+  end
+  private :auto_parse
+
+  # Passing a BLAST output from 'blastall -m 7' or '-m 8' as a String.
+  # Formats are auto detected.
+  def initialize(data, parser = nil)
+    @iterations = []
+    @parameters = {}
+    case parser
+    when :xmlparser		# format 7
+      xmlparser_parse(data)
+    when :rexml		# format 7
+      rexml_parse(data)
+    when :tab		# format 8
+      tab_parse(data)
+    else
+      auto_parse(data)
+    end
+  end
 
+  # Returns an Array of Bio::Blast::Report::Iteration objects.
+  attr_reader :iterations
+
+  # Returns a Hash containing execution parameters.  Valid keys are:
+  # 'matrix', 'expect', 'include', 'sc-match', 'sc-mismatch',
+  # 'gap-open', 'gap-extend', 'filter'
+  attr_reader :parameters
+
+  # Shortcut for BlastOutput values.
+  attr_reader :program, :version, :reference, :db, :query_id, :query_def, :query_len
+
+  # Matrix used (-M) : shortcuts for @parameters
+  def matrix;       @parameters['matrix'];           end
+  # Expectation threshold (-e) : shortcuts for @parameters
+  def expect;       @parameters['expect'].to_i;      end
+  # Inclusion threshold (-h) : shortcuts for @parameters
+  def inclusion;    @parameters['include'].to_i;     end
+  # Match score for NT (-r) : shortcuts for @parameters
+  def sc_match;     @parameters['sc-match'].to_i;    end
+  # Mismatch score for NT (-q) : shortcuts for @parameters
+  def sc_mismatch;  @parameters['sc-mismatch'].to_i; end
+  # Gap opening cost (-G) : shortcuts for @parameters
+  def gap_open;     @parameters['gap-open'].to_i;    end
+  # Gap extension cost (-E) : shortcuts for @parameters
+  def gap_extend;   @parameters['gap-extend'].to_i;  end
+  # Filtering options (-F) : shortcuts for @parameters
+  def filter;       @parameters['filter'];           end
+  # PHI-BLAST pattern : shortcuts for @parameters
+  def pattern;      @parameters['pattern'];          end
+  # Limit of request to Entrez : shortcuts for @parameters
+  def entrez_query; @parameters['entrez-query'];     end
+
+  # Iterates on each Bio::Blast::Report::Iteration object. (for blastpgp)
+  def each_iteration
+    @iterations.each do |x|
+      yield x
+    end
+  end
 
-      # Bio::Blast::Report::Iteration
-      class Iteration
-        def initialize
-          @message = nil
-          @statistics = {}
-          @num = 1
-          @hits = []
-        end
-        attr_reader :hits, :statistics
-        attr_accessor :num, :message
+  # Iterates on each Bio::Blast::Report::Hit object of the the last Iteration.
+  # Shortcut for the last iteration's hits (for blastall)
+  def each_hit
+    @iterations.last.each do |x|
+      yield x
+    end
+  end
+  alias each each_hit
 
-        def each
-          @hits.each do |x|
-            yield x
-          end
-        end
-      end
+  # Returns a Array of Bio::Blast::Report::Hits of the last iteration.
+  # Shortcut for the last iteration's hits
+  def hits
+    @iterations.last.hits
+  end
 
+  # Returns a Hash containing execution statistics of the last iteration.
+  # Valid keys are:
+  # 'db-num', 'db-len', 'hsp-len', 'eff-space', 'kappa', 'lambda', 'entropy'
+  # Shortcut for the last iteration's statistics.
+  def statistics
+    @iterations.last.statistics
+  end
 
-      # Bio::Blast::Report::Hit
-      class Hit
-        def initialize
-          @hsps = []
-        end
-        attr_reader :hsps
-        attr_accessor :query_id, :query_def, :query_len,
-          :num, :hit_id, :len, :definition, :accession
-
-        def each
-          @hsps.each do |x|
-            yield x
-          end
-        end
+  # Number of sequences in BLAST db
+  def db_num;    statistics['db-num'];    end
+  # Length of BLAST db
+  def db_len;    statistics['db-len'];    end
+  # Effective HSP length
+  def hsp_len;   statistics['hsp-len'];   end
+  # Effective search space
+  def eff_space; statistics['eff-space']; end
+  # Karlin-Altschul parameter K
+  def kappa;     statistics['kappa'];     end
+  # Karlin-Altschul parameter Lamba
+  def lambda;    statistics['lambda'];    end
+  # Karlin-Altschul parameter H
+  def entropy;   statistics['entropy'];   end
+
+  # Returns a String (or nil) containing execution message of the last
+  # iteration (typically "CONVERGED").
+  # Shortcut for the last iteration's message (for checking 'CONVERGED')
+  def message
+    @iterations.last.message
+  end
 
-        # Compatible with Bio::Fasta::Report::Hit
 
-        alias target_id accession
-        alias target_def definition
-        alias target_len len
+  # Bio::Blast::Report::Iteration
+  class Iteration
+    def initialize
+      @message = nil
+      @statistics = {}
+      @num = 1
+      @hits = []
+    end
+    # Returns an Array of Bio::Blast::Report::Hit objects.
+    attr_reader :hits
 
-        # Shortcut methods for the best Hsp
+    # Returns a Hash containing execution statistics.
+    # Valid keys are:
+    # 'db-len', 'db-num', 'eff-space', 'entropy', 'hsp-len', 'kappa', 'lambda'
+    attr_reader :statistics
 
-        def evalue;		@hsps.first.evalue;		end
-        def bit_score;		@hsps.first.bit_score;		end
-        def identity;		@hsps.first.identity;		end
-        def percent_identity;	@hsps.first.percent_identity;	end
-        def overlap;		@hsps.first.align_len;		end
+    # Returns the number of iteration counts.
+    attr_accessor :num
 
-        def query_seq;		@hsps.first.qseq;		end
-        def target_seq;		@hsps.first.hseq;		end
-        def midline;		@hsps.first.midline;		end
+    # Returns a String (or nil) containing execution message (typically
+    # "CONVERGED").
+    attr_accessor :message
 
-        def query_start;	@hsps.first.query_from;		end
-        def query_end;		@hsps.first.query_to;		end
-        def target_start;	@hsps.first.hit_from;		end
-        def target_end;		@hsps.first.hit_to;		end
-        def lap_at
-          [ query_start, query_end, target_start, target_end ]
-        end
+    # Iterates on each Bio::Blast::Report::Hit object.
+    def each
+      @hits.each do |x|
+        yield x
       end
+    end
+  end
 
 
-      # Bio::Blast::Report::Hsp
-      class Hsp
-        def initialize
-          @hsp = {}
-        end
-        attr_reader :hsp
-        attr_accessor :num, :bit_score, :score, :evalue,
-          :query_from, :query_to, :hit_from, :hit_to,
-          :pattern_from, :pattern_to, :query_frame, :hit_frame,
-          :identity, :positive, :gaps, :align_len, :density,
-          :qseq, :hseq, :midline,
-          :percent_identity, :mismatch_count	 # only for '-m 8'
+  # Bio::Blast::Report::Hit
+  class Hit
+    def initialize
+      @hsps = []
+    end
+
+    # Returns an Array of Bio::Blast::Report::Hsp objects.
+    attr_reader :hsps
+
+    # Hit number
+    attr_accessor :num
+    # SeqId of subject
+    attr_accessor :hit_id
+    # Length of subject
+    attr_accessor :len
+    # Definition line of subject
+    attr_accessor :definition
+    # Accession
+    attr_accessor :accession
+
+    # Iterates on each Hsp object.
+    def each
+      @hsps.each do |x|
+        yield x
       end
+    end
 
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    attr_accessor :query_id
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    attr_accessor :query_def
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    attr_accessor :query_len
+
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    alias target_id accession
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    alias target_def definition
+    # Compatible method with Bio::Fasta::Report::Hit class.
+    alias target_len len
+
+    # Shortcut methods for the best Hsp, some are also compatible with
+    # Bio::Fasta::Report::Hit class.
+    def evalue;           @hsps.first.evalue;           end
+    def bit_score;        @hsps.first.bit_score;        end
+    def identity;         @hsps.first.identity;         end
+    def percent_identity; @hsps.first.percent_identity; end
+    def overlap;          @hsps.first.align_len;        end
+
+    def query_seq;        @hsps.first.qseq;             end
+    def target_seq;       @hsps.first.hseq;             end
+    def midline;          @hsps.first.midline;          end
+
+    def query_start;      @hsps.first.query_from;       end
+    def query_end;        @hsps.first.query_to;         end
+    def target_start;     @hsps.first.hit_from;         end
+    def target_end;       @hsps.first.hit_to;           end
+    def lap_at
+      [ query_start, query_end, target_start, target_end ]
     end
   end
-end
+
+
+  # Bio::Blast::Report::Hsp
+  class Hsp
+    def initialize
+      @hsp = {}
+    end
+    attr_reader :hsp
+
+    # HSP number
+    attr_accessor :num
+    # Score (in bits) of HSP
+    attr_accessor :bit_score
+    # Sscore of HSP
+    attr_accessor :score
+    # E-value of HSP
+    attr_accessor :evalue
+    # Start of HSP in query
+    attr_accessor :query_from
+    # End of HSP
+    attr_accessor :query_to
+    # Start of HSP in subject
+    attr_accessor :hit_from
+    # End of HSP
+    attr_accessor :hit_to
+    # Start of PHI-BLAST pattern
+    attr_accessor :pattern_from
+    # End of PHI-BLAST pattern
+    attr_accessor :pattern_to
+    # Translation frame of query
+    attr_accessor :query_frame
+    # Translation frame of subject
+    attr_accessor :hit_frame
+    # Number of identities in HSP
+    attr_accessor :identity
+    # Number of positives in HSP
+    attr_accessor :positive
+    # Number of gaps in HSP
+    attr_accessor :gaps
+    # Length of the alignment used
+    attr_accessor :align_len
+    # Score density
+    attr_accessor :density
+    # Alignment string for the query (with gaps)
+    attr_accessor :qseq
+    # Alignment string for subject (with gaps)
+    attr_accessor :hseq
+    # Formating middle line
+    attr_accessor :midline
+    # Available only for '-m 8' format outputs.
+    attr_accessor :percent_identity
+    # Available only for '-m 8' format outputs.
+    attr_accessor :mismatch_count
+  end
+
+end # Report
+
+end # Blast
+end # Bio
 
 
 if __FILE__ == $0
@@ -389,264 +514,3 @@ if __FILE__ == $0
 end
 
 
-=begin
-
-= Bio::Blast::Report
-
-Parsed results of the blast execution for Tab-delimited and XML output
-format.  Tab-delimited reports are consists of
-
-  Query id,
-  Subject id,
-  percent of identity,
-  alignment length,
-  number of mismatches (not including gaps),
-  number of gap openings,
-  start of alignment in query,
-  end of alignment in query,
-  start of alignment in subject,
-  end of alignment in subject,
-  expected value,
-  bit score.
-
-according to the MEGABLAST document (README.mbl).  As for XML output,
-see the following DTDs.
-
-  * http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
-  * http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod
-  * http://www.ncbi.nlm.nih.gov/dtd/NCBI_Entity.mod
-
-
---- Bio::Blast::Report.new(data)
-
-      Passing a BLAST output from 'blastall -m 7' or '-m 8' as a String.
-      Formats are auto detected.
-
---- Bio::Blast::Report.xmlparaser(xml)
-
-      Specify to use XMLParser to parse XML (-m 7) output.
-
---- Bio::Blast::Report.rexml(xml)
-
-      Specify to use REXML to parse XML (-m 7) output.
-
---- Bio::Blast::Report.tab(data)
-
-      Specify to use tab delimited output parser.
-
---- Bio::Blast::Report#program
---- Bio::Blast::Report#version
---- Bio::Blast::Report#reference
---- Bio::Blast::Report#db
---- Bio::Blast::Report#query_id
---- Bio::Blast::Report#query_def
---- Bio::Blast::Report#query_len
-
-      Shortcut for BlastOutput values.
-
---- Bio::Blast::Report#parameters
-
-      Returns a Hash containing execution parameters.  Valid keys are:
-        'matrix', 'expect', 'include', 'sc-match', 'sc-mismatch',
-        'gap-open', 'gap-extend', 'filter'
-
---- Bio::Blast::Report#matrix
-      * Matrix used (-M)
---- Bio::Blast::Report#expect
-      * Expectation threshold (-e)
---- Bio::Blast::Report#inclusion
-      * Inclusion threshold (-h)
---- Bio::Blast::Report#sc_match
-      * Match score for NT (-r)
---- Bio::Blast::Report#sc_mismatch
-      * Mismatch score for NT (-q)
---- Bio::Blast::Report#gap_open
-      * Gap opening cost (-G)
---- Bio::Blast::Report#gap_extend
-      * Gap extension cost (-E)
---- Bio::Blast::Report#filter
-      * Filtering options (-F)
---- Bio::Blast::Report#pattern
-      * PHI-BLAST pattern
---- Bio::Blast::Report#entrez_query
-      * Limit of request to Entrez
-
-      These are shortcuts for parameters.
-
-
---- Bio::Blast::Report#iterations
-
-      Returns an Array of Bio::Blast::Report::Iteration objects.
-
---- Bio::Blast::Report#each_iteration
-
-      Iterates on each Bio::Blast::Report::Iteration object.
-
---- Bio::Blast::Report#each_hit
---- Bio::Blast::Report#each
-
-      Iterates on each Bio::Blast::Report::Hit object of the the
-      last Iteration.
-
---- Bio::Blast::Report#statistics
-
-      Returns a Hash containing execution statistics of the last iteration.
-      Valid keys are:
-        'db-num', 'db-len', 'hsp-len', 'eff-space', 'kappa',
-        'lambda', 'entropy'
-
---- Bio::Blast::Report#db_num
-      * Number of sequences in BLAST db
---- Bio::Blast::Report#db_len
-      * Length of BLAST db
---- Bio::Blast::Report#hsp_len
-      * Effective HSP length
---- Bio::Blast::Report#eff_space
-      * Effective search space
---- Bio::Blast::Report#kappa
-      * Karlin-Altschul parameter K
---- Bio::Blast::Report#lambda
-      * Karlin-Altschul parameter Lamba
---- Bio::Blast::Report#entropy
-      * Karlin-Altschul parameter H
-
-      These are shortcuts for statistics.
-
-
---- Bio::Blast::Report#message
-
-      Returns a String (or nil) containing execution message of the last
-      iteration (typically "CONVERGED").
-
---- Bio::Blast::Report#hits
-
-      Returns a Array of Bio::Blast::Report::Hits of the last iteration.
-
-
-== Bio::Blast::Report::Iteration
-
---- Bio::Blast::Report::Iteration#num
-
-      Returns the number of iteration counts.
-
---- Bio::Blast::Report::Iteration#hits
-
-      Returns an Array of Bio::Blast::Report::Hit objects.
-
---- Bio::Blast::Report::Iteration#each
-
-      Iterates on each Bio::Blast::Report::Hit object.
-
---- Bio::Blast::Report::Iteration#statistics
-
-      Returns a Hash containing execution statistics.
-      Valid keys are:
-        'db-len', 'db-num', 'eff-space', 'entropy', 'hsp-len',
-        'kappa', 'lambda'
-
---- Bio::Blast::Report::Iteration#message
-
-      Returns a String (or nil) containing execution message (typically
-      "CONVERGED").
-
-
-== Bio::Blast::Report::Hit
-
---- Bio::Blast::Report::Hit#each
-
-      Iterates on each Hsp object.
-
---- Bio::Blast::Report::Hit#hsps
-
-      Returns an Array of Bio::Blast::Report::Hsp objects.
-
---- Bio::Blast::Report::Hit#num
-      * hit number
---- Bio::Blast::Report::Hit#hit_id
-      * SeqId of subject
---- Bio::Blast::Report::Hit#len
-      * length of subject
---- Bio::Blast::Report::Hit#definition
-      * definition line of subject
---- Bio::Blast::Report::Hit#accession
-      * accession
-
-      Accessors for the Hit values.
-
---- Bio::Blast::Report::Hit#query_id
---- Bio::Blast::Report::Hit#query_def
---- Bio::Blast::Report::Hit#query_len
---- Bio::Blast::Report::Hit#target_id
---- Bio::Blast::Report::Hit#target_def
---- Bio::Blast::Report::Hit#target_len
-
-      Compatible methods with Bio::Fasta::Report::Hit class.
-
---- Bio::Blast::Report::Hit#evalue
---- Bio::Blast::Report::Hit#bit_score
---- Bio::Blast::Report::Hit#identity
---- Bio::Blast::Report::Hit#overlap
-
---- Bio::Blast::Report::Hit#query_seq
---- Bio::Blast::Report::Hit#midline
---- Bio::Blast::Report::Hit#target_seq
-
---- Bio::Blast::Report::Hit#query_start
---- Bio::Blast::Report::Hit#query_end
---- Bio::Blast::Report::Hit#target_start
---- Bio::Blast::Report::Hit#target_end
---- Bio::Blast::Report::Hit#lap_at
-
-      Shortcut methods for the best Hsp, some are also compatible with
-      Bio::Fasta::Report::Hit class.
-
-
-== Bio::Blast::Report::Hsp
-
---- Bio::Blast::Report::Hsp#num
-      * HSP number
---- Bio::Blast::Report::Hsp#bit_score
-      * score (in bits) of HSP
---- Bio::Blast::Report::Hsp#score
-      * score of HSP
---- Bio::Blast::Report::Hsp#evalue
-      * e-value of HSP
---- Bio::Blast::Report::Hsp#query_from
-      * start of HSP in query
---- Bio::Blast::Report::Hsp#query_to
-      * end of HSP
---- Bio::Blast::Report::Hsp#hit_from
-      * start of HSP in subject
---- Bio::Blast::Report::Hsp#hit_to
-      * end of HSP
---- Bio::Blast::Report::Hsp#pattern_from
-      * start of PHI-BLAST pattern
---- Bio::Blast::Report::Hsp#pattern_to
-      * end of PHI-BLAST pattern
---- Bio::Blast::Report::Hsp#query_frame
-      * translation frame of query
---- Bio::Blast::Report::Hsp#hit_frame
-      * translation frame of subject
---- Bio::Blast::Report::Hsp#identity
-      * number of identities in HSP
---- Bio::Blast::Report::Hsp#positive
-      * number of positives in HSP
---- Bio::Blast::Report::Hsp#gaps
-      * number of gaps in HSP
---- Bio::Blast::Report::Hsp#align_len
-      * length of the alignment used
---- Bio::Blast::Report::Hsp#density
-      * score density
---- Bio::Blast::Report::Hsp#qseq
-      * alignment string for the query (with gaps)
---- Bio::Blast::Report::Hsp#hseq
-      * alignment string for subject (with gaps)
---- Bio::Blast::Report::Hsp#midline
-      * formating middle line
-
---- Bio::Blast::Report::Hsp#percent_identity
---- Bio::Blast::Report::Hsp#mismatch_count
-
-      Available only for '-m 8' format outputs.
-
-=end