[BioRuby-cvs] bioruby/lib/bio/appl/fasta format10.rb, 1.3, 1.4 format6.rb, 1.1, 1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/fasta
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/appl/fasta

Modified Files:
	format10.rb format6.rb 
Log Message:
* expanded tab at the line head


Index: format10.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta/format10.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** format10.rb	3 Feb 2003 14:29:47 -0000	1.3
--- format10.rb	8 Sep 2005 01:22:09 -0000	1.4
***************
*** 27,259 ****
  
        def initialize(data)
! 	# header lines - brief list of the hits
          if data.sub!(/.*\nThe best scores are/m, '')
! 	  data.sub!(/(.*)\n\n>>>/m, '')
! 	  @list = "The best scores are" + $1
! 	else
! 	  data.sub!(/.*\n!!\s+/m, '')
! 	  data.sub!(/.*/) { |x| @list = x; '' }
! 	end
  
! 	# body lines - fasta execution result
! 	program, *hits = data.split(/\n>>/)
  
! 	# trailing lines - log messages of the execution
! 	@log = hits.pop
          @log.sub!(/.*<\n/m, '')
          @log.strip!
  
! 	# parse results
! 	@program = Program.new(program)
! 	@hits = []
  
! 	hits.each do |x|
! 	  @hits.push(Hit.new(x))
! 	end
        end
        attr_reader :list, :log, :program, :hits
  
        def each
! 	@hits.each do |x|
! 	  yield x
! 	end
        end
  
        def threshold(evalue_max = 0.1)
! 	list = []
! 	@hits.each do |x|
! 	  list.push(x) if x.evalue < evalue_max
! 	end
! 	return list
        end
  
        def lap_over(length_min = 0)
! 	list = []
! 	@hits.each do |x|
! 	  list.push(x) if x.overlap > length_min
! 	end
! 	return list
        end
  
  
        class Program
! 	def initialize(data)
! 	  @definition, *program = data.split(/\n/)
! 	  @program = {}
  
! 	  pat = /;\s+([^:]+):\s+(.*)/
  
! 	  program.each do |x|
! 	    if pat.match(x)
! 	      @program[$1] = $2
! 	    end
! 	  end
! 	end
! 	attr_reader :definition, :program
        end
  
  
        class Hit
! 	def initialize(data)
! 	  score, query, target = data.split(/\n>/)
  
! 	  @definition, *score = score.split(/\n/)
! 	  @score = {}
  
! 	  pat = /;\s+([^:]+):\s+(.*)/
  
! 	  score.each do |x|
! 	    if pat.match(x)
! 	      @score[$1] = $2
! 	    end
! 	  end
  
! 	  @query = Query.new(query)
! 	  @target = Target.new(target)
! 	end
! 	attr_reader :definition, :score, :query, :target
  
! 	def evalue
! 	  if @score['fa_expect']
! 	    @score['fa_expect'].to_f
! 	  elsif @score['sw_expect']
! 	    @score['sw_expect'].to_f
! 	  elsif @score['fx_expect']
! 	    @score['fx_expect'].to_f
! 	  elsif @score['tx_expect']
! 	    @score['tx_expect'].to_f
! 	  end
! 	end
  
! 	def bit_score
! 	  if @score['fa_bits']
! 	    @score['fa_bits'].to_f
! 	  elsif @score['sw_bits']
! 	    @score['sw_bits'].to_f
! 	  elsif @score['fx_bits']
! 	    @score['fx_bits'].to_f
! 	  elsif @score['tx_bits']
! 	    @score['tx_bits'].to_f
! 	  end
! 	end
  
! 	def direction
! 	  @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
! 	end
  
! 	def sw
! 	  @score['sw_score'].to_i
! 	end
  
! 	def identity
! 	  @score['sw_ident'].to_f
! 	end
  
! 	def overlap
! 	  @score['sw_overlap'].to_i
! 	end
  
! 	def query_id
! 	  @query.entry_id
! 	end
  
! 	def target_id
! 	  @target.entry_id
! 	end
  
! 	def query_def
! 	  @query.definition
! 	end
  
! 	def target_def
! 	  @target.definition
! 	end
  
! 	def query_len
! 	  @query.length
! 	end
  
! 	def target_len
! 	  @target.length
! 	end
  
! 	def query_seq
! 	  @query.sequence
! 	end
  
! 	def target_seq
! 	  @target.sequence
! 	end
  
! 	def query_type
! 	  @query.moltype
! 	end
  
! 	def target_type
! 	  @target.moltype
! 	end
  
! 	def query_start
! 	  @query.start
! 	end
  
! 	def query_end
! 	  @query.stop
! 	end
  
! 	def target_start
! 	  @target.start
! 	end
  
! 	def target_end
! 	  @target.stop
! 	end
  
! 	def lap_at
! 	  [ query_start, query_end, target_start, target_end ]
! 	end
  
  
! 	class Query
! 	  def initialize(data)
! 	    @definition, *data = data.split(/\n/)
! 	    @data = {}
! 	    @sequence = ''
  
! 	    pat = /;\s+([^:]+):\s+(.*)/
  
! 	    data.each do |x|
! 	      if pat.match(x)
! 		@data[$1] = $2
! 	      else
! 		@sequence += x
! 	      end
! 	    end
! 	  end
! 	  attr_reader :definition, :data, :sequence
  
! 	  def entry_id
! 	    @definition[/\S+/]
! 	  end
  
! 	  def length
! 	    @data['sq_len'].to_i
! 	  end
  
! 	  def moltype
! 	    @data['sq_type']
! 	  end
  
! 	  def start
! 	    @data['al_start'].to_i
! 	  end
  
! 	  def stop
! 	    @data['al_stop'].to_i
! 	  end
  
! 	end
  
! 	class Target < Query; end
        end
  
--- 27,259 ----
  
        def initialize(data)
!         # header lines - brief list of the hits
          if data.sub!(/.*\nThe best scores are/m, '')
!           data.sub!(/(.*)\n\n>>>/m, '')
!           @list = "The best scores are" + $1
!         else
!           data.sub!(/.*\n!!\s+/m, '')
!           data.sub!(/.*/) { |x| @list = x; '' }
!         end
  
!         # body lines - fasta execution result
!         program, *hits = data.split(/\n>>/)
  
!         # trailing lines - log messages of the execution
!         @log = hits.pop
          @log.sub!(/.*<\n/m, '')
          @log.strip!
  
!         # parse results
!         @program = Program.new(program)
!         @hits = []
  
!         hits.each do |x|
!           @hits.push(Hit.new(x))
!         end
        end
        attr_reader :list, :log, :program, :hits
  
        def each
!         @hits.each do |x|
!           yield x
!         end
        end
  
        def threshold(evalue_max = 0.1)
!         list = []
!         @hits.each do |x|
!           list.push(x) if x.evalue < evalue_max
!         end
!         return list
        end
  
        def lap_over(length_min = 0)
!         list = []
!         @hits.each do |x|
!           list.push(x) if x.overlap > length_min
!         end
!         return list
        end
  
  
        class Program
!         def initialize(data)
!           @definition, *program = data.split(/\n/)
!           @program = {}
  
!           pat = /;\s+([^:]+):\s+(.*)/
  
!           program.each do |x|
!             if pat.match(x)
!               @program[$1] = $2
!             end
!           end
!         end
!         attr_reader :definition, :program
        end
  
  
        class Hit
!         def initialize(data)
!           score, query, target = data.split(/\n>/)
  
!           @definition, *score = score.split(/\n/)
!           @score = {}
  
!           pat = /;\s+([^:]+):\s+(.*)/
  
!           score.each do |x|
!             if pat.match(x)
!               @score[$1] = $2
!             end
!           end
  
!           @query = Query.new(query)
!           @target = Target.new(target)
!         end
!         attr_reader :definition, :score, :query, :target
  
!         def evalue
!           if @score['fa_expect']
!             @score['fa_expect'].to_f
!           elsif @score['sw_expect']
!             @score['sw_expect'].to_f
!           elsif @score['fx_expect']
!             @score['fx_expect'].to_f
!           elsif @score['tx_expect']
!             @score['tx_expect'].to_f
!           end
!         end
  
!         def bit_score
!           if @score['fa_bits']
!             @score['fa_bits'].to_f
!           elsif @score['sw_bits']
!             @score['sw_bits'].to_f
!           elsif @score['fx_bits']
!             @score['fx_bits'].to_f
!           elsif @score['tx_bits']
!             @score['tx_bits'].to_f
!           end
!         end
  
!         def direction
!           @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame']
!         end
  
!         def sw
!           @score['sw_score'].to_i
!         end
  
!         def identity
!           @score['sw_ident'].to_f
!         end
  
!         def overlap
!           @score['sw_overlap'].to_i
!         end
  
!         def query_id
!           @query.entry_id
!         end
  
!         def target_id
!           @target.entry_id
!         end
  
!         def query_def
!           @query.definition
!         end
  
!         def target_def
!           @target.definition
!         end
  
!         def query_len
!           @query.length
!         end
  
!         def target_len
!           @target.length
!         end
  
!         def query_seq
!           @query.sequence
!         end
  
!         def target_seq
!           @target.sequence
!         end
  
!         def query_type
!           @query.moltype
!         end
  
!         def target_type
!           @target.moltype
!         end
  
!         def query_start
!           @query.start
!         end
  
!         def query_end
!           @query.stop
!         end
  
!         def target_start
!           @target.start
!         end
  
!         def target_end
!           @target.stop
!         end
  
!         def lap_at
!           [ query_start, query_end, target_start, target_end ]
!         end
  
  
!         class Query
!           def initialize(data)
!             @definition, *data = data.split(/\n/)
!             @data = {}
!             @sequence = ''
  
!             pat = /;\s+([^:]+):\s+(.*)/
  
!             data.each do |x|
!               if pat.match(x)
!                 @data[$1] = $2
!               else
!                 @sequence += x
!               end
!             end
!           end
!           attr_reader :definition, :data, :sequence
  
!           def entry_id
!             @definition[/\S+/]
!           end
  
!           def length
!             @data['sq_len'].to_i
!           end
  
!           def moltype
!             @data['sq_type']
!           end
  
!           def start
!             @data['al_start'].to_i
!           end
  
!           def stop
!             @data['al_stop'].to_i
!           end
  
!         end
  
!         class Target < Query; end
        end
  

Index: format6.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta/format6.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** format6.rb	28 May 2002 14:49:07 -0000	1.1
--- format6.rb	8 Sep 2005 01:22:09 -0000	1.2
***************
*** 29,33 ****
  
        def initialize
! 	raise NotImplementedError
        end
      end
--- 29,33 ----
  
        def initialize
!         raise NotImplementedError
        end
      end