bio 1.2.1 → 1.3.0

data/doc/bioruby.css

@@ -0,0 +1,281 @@
+/* body */
+
+body {
+	color: #000000;
+	background-color: #ffffff;
+	margin-left: 5%;
+	margin-right: 5%;
+	font-family: verdana, arial;
+}
+
+em {
+	font-weight: bold;
+	font-style: normal;
+}
+
+/* link */
+
+a:link {
+	color: #00ca65;
+	text-decoration: none;
+}
+a:visited {
+	color: #49ba18;
+	text-decoration: none;
+}
+a:hover, a:focus {
+	color: #c2fe20;
+	background-color: #ffffff;
+	text-decoration: underline;
+}
+
+
+/* header */
+
+h1 {     
+	color: #000000;
+	background-color: transparent;
+	border-color: #49ba18; 
+/*	border-width: 1px 0px 1px 0px;*/
+	border-width: 0px 0px 5px 0px;
+	border-style: solid;
+	padding-bottom: 3px;
+	padding-right: 10%;
+	text-align: left;
+}
+h2 {
+	color: #000000;
+/*	background-color: transparent;*/
+	background-color: #b0ffb0;
+	border-color: #b0ffb0;
+	border-style: none;
+	border-width: 1px 0px 1px 0px;
+	margin-bottom: 0px;
+	margin-top: 1em;
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+}
+h3 {
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+	font-weight: bold;
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+	border-color: #d8ffd8;
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+	border-width: 2px 0px 0px 2px;
+}
+h4 {
+	padding-bottom: 1px;
+	padding-left: 5px;
+	font-weight: bold;
+	font-weight: bold;
+	border-style: solid;
+	border-color: #b0ffb0;
+	border-width: 0px 0px 2px 0px;
+/*	margin: 1.5em 10px 0px*/
+}
+h5 {
+	padding-top: 2px;
+	padding-left: 5px;
+	font-weight: bold;
+	border-style: dotted;
+	border-color: #d8ffd8;
+	border-width: 2px 0px 0px 2px;
+/*	margin: 1.5em 20px 0px*/
+}
+h6 {
+	padding-left: 5px;
+	font-weight: bold;
+	border-style: solid;
+	border-color: #b0ffb0;
+	border-width: 0px 0px 0px 5px;
+/*	margin: 1.5em 20px 0px*/
+}
+
+
+/* paragraph */
+
+p {
+	margin-left: 0em! important;
+	text-indent: 0em
+}
+
+
+/* line */
+
+hr {
+	border-style: solid;
+	border-color: #00ca65;
+	border-width: 1px;
+}
+
+
+/* list */
+
+dl {
+}
+dt {
+	padding-left: 5px;
+	font-size: 110%;
+	border-style: solid;
+	border-color: #B0FFB0;
+	border-width: 0px 0px 0px 5px;
+	font-weight: bold;
+}
+dd {
+}
+li {
+	/* list-style-type: disc; */
+}
+ul,ol{
+}
+
+
+/* table */
+
+th {
+	padding: 5px;
+	text-align: left;
+}
+td {
+	padding: 5px;
+}
+
+/* quote */
+
+pre {
+	color: #000000;
+	background-color: #d8ffd8;
+	margin-left: 20px;
+	padding: 8px;
+	border-style: solid;
+	border-color: #b0ffb0;
+	border-width: 1px 5px 1px 5px;
+	white-space: pre;
+}
+blockquote {
+	color: #008080;
+	background-color: #ffffff;
+	margin-left: 20px;
+	padding: 8px;
+	border-style: solid;
+	border-color: #38c868;
+	border-width: 3px 1px 3px 1px;
+}
+
+
+/* image */
+
+img {
+	border-width: 0px;
+}
+
+
+/* form */
+
+input, select {
+	color: #000000;
+	background-color: transparent;
+	padding: 2px;
+	border-style: solid;
+	border-color: #71e63e;
+	border-width: 1px;
+}
+textarea {
+	color: #000000;
+	background-color: #ffffff;
+	border-style: solid;
+	border-color: #00ca65;
+	border-width: 1px;
+	font-family: monospace;
+}
+
+/* reviz */
+
+table.reviz {
+	width: 100%;
+}
+th.file {
+	background-color: #008080;
+	width: 15%;
+}
+th.rev, th.age, th.author {
+	background-color: #38c868;
+	width: 10%;
+}
+th.log {
+	background-color: #c2fe20;
+}
+
+td.dir {
+	background-color: #b0ffb0;
+	background-image: url(reviz/dir.gif);
+	background-position: center left;
+	background-repeat: no-repeat;
+	text-indent: 15px;
+}
+td.file {
+	background-color: #b0ffb0;
+	background-image: url(reviz/file.gif);
+	background-position: center left;
+	background-repeat: no-repeat;
+	text-indent: 15px;
+}
+td.rev, td.age, td.author, td.log {
+	background-color: #d8ffd8;
+}
+
+
+/* rwiki */
+
+.navi {
+	text-align: right;
+}
+.headerURL {
+	text-align: right;
+	font-size: 10pt;
+}
+address {
+	color: gray;
+	text-align: right;
+	font-style: normal;
+	font-variant: normal;
+	font-weight: normal;
+}
+
+/* hiki */
+
+ins.added {
+	font-weight: bold;
+}
+del.deleted {
+	text-decoration: line-through;
+}
+form.update textarea.keyword {
+	width: 15em;
+	height: 3em;
+}
+div.adminmenu {
+	text-align: right;
+}
+div.caption {
+	text-align: right;
+}
+div.footer {
+	text-align: right;
+}
+
+
+/* top */
+
+span.title {
+	font-size: +2
+}
+span.lead {
+	text-decoration: underline
+}
+span.expire {
+	color: #c04040
+}
+span.ruby {
+	font-weight: bold
+}

data/extconf.rb

@@ -0,0 +1,2 @@
+require 'mkmf'
+create_makefile("bioruby")

data/lib/bio.rb

@@ -5,18 +5,29 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: bio.rb,v 1.88 2007/12/29 19:19:07 k Exp $
+# $Id:$
 #
 
 module Bio
 
-  BIORUBY_VERSION = [1, 2, 1].extend(Comparable)
+  autoload :BIORUBY_VERSION, 'bio/version'
+  autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
+  autoload :BIORUBY_VERSION_ID, 'bio/version'
 
   ### Basic data types
 
   ## Sequence
 
   autoload :Sequence,       'bio/sequence'
+  ## below are described in bio/sequence.rb
+  #class Sequence
+  #  autoload :Common,  'bio/sequence/common'
+  #  autoload :NA,      'bio/sequence/na'
+  #  autoload :AA,      'bio/sequence/aa'
+  #  autoload :Generic, 'bio/sequence/generic'
+  #  autoload :Format,  'bio/sequence/format'
+  #  autoload :Adapter, 'bio/sequence/adapter'
+  #end
 
   ## Locations/Location
 
@@ -26,12 +37,12 @@ module Bio
   ## Features/Feature
 
   autoload :Feature,        'bio/feature'
-  autoload :Features,       'bio/feature'
+  autoload :Features,       'bio/compat/features'
 
   ## References/Reference
 
   autoload :Reference,      'bio/reference'
-  autoload :References,     'bio/reference'
+  autoload :References,     'bio/compat/references'
 
   ## Pathway/Relation
 
@@ -144,6 +155,7 @@ module Bio
   autoload :DBGET,          'bio/io/dbget'
 
   autoload :Ensembl,        'bio/io/ensembl'
+  autoload :Hinv,           'bio/io/hinv'
 
   ## below are described in bio/appl/blast.rb
   #class Blast
@@ -169,8 +181,10 @@ module Bio
 
   class NCBI
     autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
   end
 
+  autoload :TogoWS,       'bio/io/togows'
 
   ### Applications
 
@@ -188,6 +202,9 @@ module Bio
   #  autoload :Default,      'bio/appl/blast/format0'
   #  autoload :WU,           'bio/appl/blast/wublast'
   #  autoload :Bl2seq,       'bio/appl/bl2seq/report'
+  #  autoload :RPSBlast,     'bio/appl/blast/rpsblast'
+  #  autoload :NCBIOptions,  'bio/appl/blast/ncbioptions'
+  #  autoload :Remote,       'bio/appl/blast/remote'
   #end
 
   autoload :HMMER,          'bio/appl/hmmer'
@@ -251,6 +268,14 @@ module Bio
 
   autoload :Iprscan,        'bio/appl/iprscan/report'
 
+  autoload :PAML,           'bio/appl/paml/common'
+  ## below are described in bio/appl/paml/common.rb
+  # module PAML
+  #   autoload :Codeml,         'bio/appl/paml/codeml'
+  #   autoload :Baseml,         'bio/appl/paml/baseml'
+  #   autoload :Yn00,           'bio/appl/paml/yn00'
+  # end
+
   ### Utilities
 
   autoload :SiRNA,          'bio/util/sirna'

data/lib/bio/appl/blast.rb

@@ -1,18 +1,19 @@
 #
 # = bio/appl/blast.rb - BLAST wrapper
 # 
-# Copyright::  Copyright (C) 2001       Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2001,2008  Mitsuteru C. Nakao <n@bioruby.org>
 # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k@bioruby.org>
 # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# Copyright::  Copyright (C) 2008       Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: blast.rb,v 1.33 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
-require 'net/http'
-require 'cgi' unless defined?(CGI)
 require 'bio/command'
 require 'shellwords'
+require 'stringio'
+require 'bio/io/flatfile'
 
 module Bio
 
@@ -39,20 +40,6 @@ module Bio
   #
   #   # Then, to parse the report, see Bio::Blast::Report
   #
-  # === Available databases for Bio::Blast.remote
-  #
-  #  ----------+-------+---------------------------------------------------
-  #   program  | query | db (supported in GenomeNet)
-  #  ----------+-------+---------------------------------------------------
-  #   blastp   | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
-  #  ----------+-------+ pir, prf, pdbstr
-  #   blastx   | NA    | 
-  #  ----------+-------+---------------------------------------------------
-  #   blastn   | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
-  #  ----------+-------+ htgs, dbsts, embl-nonst, embnonst-upd, epd,
-  #   tblastn  | AA    | genes-nt, genome, vgenes.nuc
-  #  ----------+-------+---------------------------------------------------
-  #
   # == See also
   #
   # * Bio::Blast::Report
@@ -69,9 +56,13 @@ module Bio
 
     autoload :Fastacmd,     'bio/io/fastacmd'
     autoload :Report,       'bio/appl/blast/report'
+    autoload :Report_tab,   'bio/appl/blast/report'
     autoload :Default,      'bio/appl/blast/format0'
     autoload :WU,           'bio/appl/blast/wublast'
     autoload :Bl2seq,       'bio/appl/bl2seq/report'
+    autoload :RPSBlast,     'bio/appl/blast/rpsblast'
+    autoload :NCBIOptions,  'bio/appl/blast/ncbioptions'
+    autoload :Remote,       'bio/appl/blast/remote'
 
     # This is a shortcut for Bio::Blast.new:
     #  Bio::Blast.local(program, database, options)
@@ -83,9 +74,14 @@ module Bio
     # * _db_ (required): name of the local database
     # * _options_: blastall options \
     # (see http://www.genome.jp/dbget-bin/show_man?blast2)
+    # * _blastall_: full path to blastall program (e.g. "/opt/bin/blastall"; DEFAULT: "blastall")
     # *Returns*:: Bio::Blast factory object
-    def self.local(program, db, option = '')
-      self.new(program, db, option, 'local')
+    def self.local(program, db, options = '', blastall = nil)
+      f = self.new(program, db, options, 'local')
+      if blastall then
+        f.blastall = blastall
+      end
+      f
     end
 
     # Bio::Blast.remote does exactly the same as Bio::Blast.new, but sets
@@ -102,17 +98,143 @@ module Bio
       self.new(program, db, option, server)
     end
 
-    # the method Bio::Blast.report is moved from bio/appl/blast/report.rb.
-    # only for xml format
+ 
+    # Bio::Blast.report parses given data, 
+    # and returns an array of report 
+    # (Bio::Blast::Report or Bio::Blast::Default::Report) objects,
+    # or yields each report object when a block is given.
+    #
+    # Supported formats: NCBI default (-m 0), XML (-m 7), tabular (-m 8).
+    #
+    # ---
+    # *Arguments*:
+    # * _input_ (required): input data
+    # * _parser_: type of parser. see Bio::Blast::Report.new
+    # *Returns*:: Undefiend when a block is given. Otherwise, an Array containing report (Bio::Blast::Report or Bio::Blast::Default::Report) objects.
     def self.reports(input, parser = nil)
+      begin
+        istr = input.to_str
+      rescue NoMethodError
+        istr = nil
+      end
+      if istr then
+        input = StringIO.new(istr)
+      end
+      raise 'unsupported input data type' unless input.respond_to?(:gets)
+
+      # if proper parser is given, emulates old behavior.
+      case parser
+      when :xmlparser, :rexml
+        ff = Bio::FlatFile.new(Bio::Blast::Report, input)
+        if block_given? then
+          ff.each do |e|
+            yield e
+          end
+          return []
+        else
+          return ff.to_a
+        end
+      when :tab
+        istr = input.read unless istr
+        rep = Report.new(istr, parser)
+        if block_given? then
+          yield rep
+          return []
+        else
+          return [ rep ]
+        end
+      end
+
+      # preparation of the new format autodetection rule if needed
+      if !defined?(@@reports_format_autodetection_rule) or
+          !@@reports_format_autodetection_rule then
+        regrule = Bio::FlatFile::AutoDetect::RuleRegexp
+        blastxml = regrule[ 'Bio::Blast::Report',
+                            /\<\!DOCTYPE BlastOutput PUBLIC / ]
+        blast    = regrule[ 'Bio::Blast::Default::Report',
+                            /^BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ]
+        tblast   = regrule[ 'Bio::Blast::Default::Report_TBlast',
+                            /^TBLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ]
+        tab      = regrule[ 'Bio::Blast::Report_tab',
+                            /^([^\t]*\t){11}[^\t]*$/ ]
+        auto = Bio::FlatFile::AutoDetect[ blastxml,
+                                          blast,
+                                          tblast,
+                                          tab
+                                        ]
+        # sets priorities
+        blastxml.is_prior_to blast
+        blast.is_prior_to tblast
+        tblast.is_prior_to tab
+        # rehash
+        auto.rehash
+        @@report_format_autodetection_rule = auto
+      end
+
+      # Creates a FlatFile object with dummy class
+      ff = Bio::FlatFile.new(Object, input)
+      ff.dbclass = nil
+
+      # file format autodetection
+      3.times do
+        break if ff.eof? or
+          ff.autodetect(31, @@report_format_autodetection_rule)
+      end
+      # If format detection failed, assumed to be tabular (-m 8)
+      ff.dbclass = Bio::Blast::Report_tab unless ff.dbclass
+
+      if block_given? then
+        ff.each do |entry|
+          yield entry
+        end
+        ret = []
+      else
+        ret = ff.to_a
+      end
+      ret
+    end
+
+    #--
+    # the method Bio::Blast.reports is moved from bio/appl/blast/report.rb.
+    #++
+     
+    # Note that this is the old implementation of Bio::Blast.reports.
+    # The aim of this method is keeping compatibility for older BLAST
+    # XML documents which might not be parsed by the new
+    # Bio::Blast.reports nor Bio::FlatFile.
+    # (Though we are not sure whether such documents exist or not.)
+    #
+    # Bio::Blast.reports_xml parses given data, 
+    # and returns an array of Bio::Blast::Report objects, or
+    # yields each Bio::Blast::Report object when a block is given.
+    #
+    # It can be used only for XML format.
+    # For default (-m 0) format, consider using Bio::FlatFile, or
+    # Bio::Blast.reports.
+    #
+    # ---
+    # *Arguments*:
+    # * _input_ (required): input data
+    # * _parser_: type of parser. see Bio::Blast::Report.new
+    # *Returns*:: Undefiend when a block is given. Otherwise, an Array containing Bio::Blast::Report objects.
+    def self.reports_xml(input, parser = nil)
       ary = []
-      input.each("</BlastOutput>\n") do |xml|
+      input.each_line("</BlastOutput>\n") do |xml|
         xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
         next if xml.empty?          # skip trailing no hits
-        if block_given?
-          yield Report.new(xml, parser)
+        rep = Report.new(xml, parser)
+        if rep.reports then
+          if block_given?
+            rep.reports.each { |r| yield r }
+          else
+            ary.concat rep.reports
+          end
         else
-          ary << Report.new(xml, parser)
+          if block_given?
+            yield rep
+          else
+            ary.push rep
+          end
         end
       end
       return ary
@@ -127,11 +249,33 @@ module Bio
     attr_accessor :db
     
     # Options for blastall
-    attr_accessor :options
+    attr_reader :options
+
+    # Sets options for blastall
+    def options=(ary)
+      @options = set_options(ary)
+    end
 
     # Server to submit the BLASTs to
     attr_accessor :server
 
+    # Sets server to submit the BLASTs to.
+    # The exec_xxxx method should be defined in Bio::Blast or
+    # Bio::Blast::Remote::Xxxx class.
+    def server=(str)
+      @server = str
+      begin
+        m = Bio::Blast::Remote.const_get(@server.capitalize)
+      rescue NameError
+        m = nil
+      end
+      if m and !(self.is_a?(m)) then
+        # lazy include Bio::Blast::Remote::XXX module
+        self.class.class_eval { include m }
+      end
+      return @server
+    end
+
     # Full path for blastall. (default: 'blastall').
     attr_accessor :blastall
 
@@ -148,7 +292,7 @@ module Bio
     #
     # 0, pairwise; 1; 2; 3; 4; 5; 6; 7, XML Blast outpu;, 8, tabular; 
     # 9, tabular with comment lines; 10, ASN text; 11, ASN binery [intege].
-    attr_reader :format
+    attr_accessor :format
 
     #
     attr_writer :parser  # to change :xmlparser, :rexml, :tab
@@ -173,7 +317,6 @@ module Bio
     def initialize(program, db, opt = [], server = 'local')
       @program  = program
       @db       = db
-      @server   = server
 
       @blastall = 'blastall'
       @matrix   = nil
@@ -181,137 +324,179 @@ module Bio
 
       @output   = ''
       @parser   = nil
+      @format   = nil
 
-      begin
-        a = opt.to_ary
-      rescue NameError #NoMethodError
-        # backward compatibility
-        a = Shellwords.shellwords(opt)
-      end
-      unless a.find { |x| /\A\-m/ =~ x.to_s } then
-        if defined?(XMLParser) or defined?(REXML)
-          @format = 7
-        else
-          @format = 8
-        end
-      end
-      @options = [ *a ]
+      @options = set_options(opt, program, db)
+      self.server = server
     end
 
+
     # This method submits a sequence to a BLAST factory, which performs the
     # actual BLAST.
     # 
-    #   fasta_sequences = Bio::FlatFile.open(Bio::FastaFormat, 'my_sequences.fa')
-    #   report = blast_factory.query(fasta_sequences)
+    #   # example 1
+    #   seq = Bio::Sequence::NA.new('agggcattgccccggaagatcaagtcgtgctcctg')
+    #   report = blast_factory.query(seq)
+    #
+    #   # example 2
+    #   str <<END_OF_FASTA
+    #   >lcl|MySequence
+    #   MPPSAISKISNSTTPQVQSSSAPNLTMLEGKGISVEKSFRVYSEEENQNQHKAKDSLGF
+    #   KELEKDAIKNSKQDKKDHKNWLETLYDQAEQKWLQEPKKKLQDLIKNSGDNSRVILKDS
+    #   END_OF_FASTA
+    #   report = blast_factory.query(str)
+    #
+    # Bug note: When multi-FASTA is given and the format is 7 (XML) or 8 (tab),
+    # it should return an array of Bio::Blast::Report objects,
+    # but it returns a single Bio::Blast::Report object.
+    # This is a known bug and should be fixed in the future.
     # 
     # ---
     # *Arguments*:
     # * _query_ (required): single- or multiple-FASTA formatted sequence(s)
-    # *Returns*:: a Bio::Blast::Report object
+    # *Returns*:: a Bio::Blast::Report (or Bio::Blast::Default::Report) object when single query is given. When multiple sequences are given as the query, it returns an array of Bio::Blast::Report (or Bio::Blast::Default::Report) objects. If it can not parse result, nil will be returnd.
     def query(query)
-      return self.send("exec_#{@server}", query.to_s)
+      case query
+      when Bio::Sequence
+        query = query.output(:fasta)
+      when Bio::Sequence::NA, Bio::Sequence::AA, Bio::Sequence::Generic
+        query = query.to_fasta('query', 70)
+      else
+        query = query.to_s
+      end
+
+      @output = self.__send__("exec_#{@server}", query)
+      report = parse_result(@output)
+      return report
     end
 
     # Returns options of blastall
     def option
       # backward compatibility
-      Bio::Command.make_command_line(@options)
+      Bio::Command.make_command_line(options)
     end
 
     # Set options for blastall
     def option=(str)
       # backward compatibility
-      @options = Shellwords.shellwords(str)
+      self.options = Shellwords.shellwords(str)
     end
 
-
     private
 
+    def set_options(opt = nil, program = nil, db = nil)
+      opt = @options unless opt
 
-    def parse_result(data)
-      Report.new(data, @parser)
-    end
-
+      # when opt is a String, splits to an array
+      begin
+        a = opt.to_ary
+      rescue NameError #NoMethodError
+        # backward compatibility
+        a = Shellwords.shellwords(opt)
+      end
+      ncbiopt = NCBIOptions.new(a)
 
-    def exec_local(query)
-      cmd = [ @blastall, '-p', @program, '-d', @db ]
-      cmd.concat([ '-M', @matrix ]) if @matrix
-      cmd.concat([ '-F', @filter ]) if @filter
-      cmd.concat([ '-m', @format.to_s ]) if @format
-      cmd.concat(@options) if @options
+      if fmt = ncbiopt.get('-m') then
+        @format = fmt.to_i
+      else
+        Bio::Blast::Report #dummy to load XMLParser or REXML
+        if defined?(XMLParser) or defined?(REXML)
+          @format ||= 7
+        else
+          @format ||= 8
+        end
+      end
 
-      report = nil
+      mtrx = ncbiopt.get('-M')
+      @matrix = mtrx if mtrx
+      fltr = ncbiopt.get('-F')
+      @filter = fltr if fltr
+
+      # special treatment for '-p'
+      if program then
+        @program = program
+        ncbiopt.delete('-p')
+      else
+        program = ncbiopt.get('-p')
+        @program = program if program
+      end
 
-      @output = Bio::Command.query_command(cmd, query)
-      report = parse_result(@output)
+      # special treatment for '-d'
+      if db then
+        @db = db
+        ncbiopt.delete('-d')
+      else
+        db = ncbiopt.get('-d')
+        @db = db if db
+      end
 
-      return report
+      # returns an array of string containing options
+      return ncbiopt.options
     end
 
-    def exec_genomenet_tab(query)
-      @format = 8
-      exec_genomenet(query)
+    # parses result
+    def parse_result(str)
+      if @format.to_i == 0 then
+        ary = Bio::FlatFile.open(Bio::Blast::Default::Report,
+                                 StringIO.new(str)) { |ff| ff.to_a }
+        case ary.size
+        when 0
+          return nil
+        when 1
+          return ary[0]
+        else
+          return ary
+        end
+      else
+        Report.new(str, @parser)
+      end
     end
 
-    def exec_genomenet(query)
-      host = "blast.genome.jp"
-      #path = "/sit-bin/nph-blast"
-      path = "/sit-bin/blast" #2005.08.12
-
-      matrix = @matrix ? @matrix : 'blosum62'
-      filter = @filter ? @filter : 'T'
-
-      opt = []
-      opt.concat([ '-m', @format.to_s ]) if @format
-      opt.concat(@options) if @options
-
-      form = {
-        'style'          => 'raw',
-        'prog'           => @program,
-        'dbname'         => @db,
-        'sequence'       => CGI.escape(query),
-        'other_param'    => CGI.escape(Bio::Command.make_command_line_unix(opt)),
-        'matrix'         => matrix,
-        'filter'         => filter,
-        'V_value'        => 500, # default value for GenomeNet
-        'B_value'        => 250, # default value for GenomeNet
-        'alignment_view' => 0,
-      }
-
-      data = []
-
-      form.each do |k, v|
-        data.push("#{k}=#{v}") if v
+    # returns an array containing NCBI BLAST options
+    def make_command_line_options
+      set_options
+      cmd = []
+      if @program
+        cmd.concat([ '-p', @program ])
       end
-
-      report = nil
-
-      begin
-        http = Bio::Command.new_http(host)
-        http.open_timeout = 300
-        http.read_timeout = 600
-        result, = http.post(path, data.join('&'))
-        @output = result.body
-        # workaround 2005.08.12
-        if /\<A +HREF=\"(http\:\/\/blast\.genome\.jp(\/tmp\/[^\"]+))\"\>Show all result\<\/A\>/i =~ @output.to_s then
-          result, = http.get($2)
-          @output = result.body
-          txt = @output.to_s.split(/\<pre\>/)[1]
-          raise 'cannot understand response' unless txt
-          txt.sub!(/\<\/pre\>.*\z/m, '')
-          txt.sub!(/.*^ \-{20,}\s*/m, '')
-          @output = txt.gsub(/\&lt\;/, '<')
-          report = parse_result(@output)
-        else
-          raise 'cannot understand response'
-        end
+      if @db
+        cmd.concat([ '-d', @db ])
+      end
+      if @format
+        cmd.concat([ '-m', @format.to_s ])
       end
+      if @matrix
+        cmd.concat([ '-M', @matrix ]) 
+      end
+      if @filter
+        cmd.concat([ '-F', @filter ]) 
+      end
+      ncbiopts = NCBIOptions.new(@options)
+      ncbiopts.make_command_line_options(cmd)
+    end
 
-      return report
+    # makes command line.
+    def make_command_line
+      cmd = make_command_line_options
+      cmd.unshift @blastall
+      cmd
+    end
+
+    # Local execution of blastall
+    def exec_local(query)
+      cmd = make_command_line
+      @output = Bio::Command.query_command(cmd, query)
+      return @output
     end
 
-    def exec_ncbi(query)
-      raise NotImplementedError
+    # This method is obsolete.
+    #
+    # Runs genomenet with '-m 8' option.
+    # Note that the format option is overwritten.
+    def exec_genomenet_tab(query)
+      warn "Bio::Blast#server=\"genomenet_tab\" is deprecated."
+      @format = 8
+      exec_genomenet(query)
     end
 
   end # class Blast