bio 1.6.0.pre.20181210 → 2.0.3

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

@@ -1,236 +0,0 @@
-#
-# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
-# 
-# Copyright::  Copyright (C) 2001 
-#              Mitsuteru C. Nakao <n@bioruby.org>
-# Copyright::  Copyright (C) 2003 
-#              Toshiaki Katayama <k@bioruby.org>
-# License::    The Ruby License
-#
-# $Id:$
-#
-# == Description
-# 
-# A parser for blast XML report (format 7) based on the XMLParser.
-# This file is automatically loaded by bio/appl/blast/report.rb if
-# the XMLParser installed.
-#
-# BioRuby provides two implements of the paser for the blast XML format report
-# (format 7) based on the XMLParser and the REXML.
-#
-
-begin
-  require 'xmlparser'
-rescue LoadError
-end
-
-module Bio
-class Blast
-  class Report
-
-    private
-
-    def xmlparser_parse(xml)
-      parser = XMLParser.new
-      def parser.default; end
-       
-      begin
-        tag_stack = Array.new
-        hash = Hash.new
-
-        parser.parse(xml) do |type, name, data|
-          case type
-          when XMLParser::START_ELEM
-            tag_stack.push(name)
-            hash.update(data)
-            case name
-            when 'Iteration'
-              iteration = Iteration.new
-              @iterations.push(iteration)
-            when 'Hit'
-              hit = Hit.new
-              hit.query_id = @query_id
-              hit.query_def = @query_def
-              hit.query_len = @query_len
-              @iterations.last.hits.push(hit)
-            when 'Hsp'
-              hsp = Hsp.new
-              @iterations.last.hits.last.hsps.push(hsp)
-            end
-          when XMLParser::END_ELEM
-            case name
-            when /^BlastOutput/
-              xmlparser_parse_program(name,hash)
-              hash = Hash.new
-            when /^Parameters$/
-              xmlparser_parse_parameters(hash)
-              hash = Hash.new
-            when /^Iteration/
-              xmlparser_parse_iteration(name, hash)
-              hash = Hash.new
-            when /^Hit/
-              xmlparser_parse_hit(name, hash)
-              hash = Hash.new
-            when /^Hsp$/
-              xmlparser_parse_hsp(hash)
-              hash = Hash.new
-            when /^Statistics$/
-              xmlparser_parse_statistics(hash)
-              hash = Hash.new
-            end
-            tag_stack.pop
-          when XMLParser::CDATA
-            if hash[tag_stack.last].nil?
-              hash[tag_stack.last] = data unless data.strip.empty?
-            else
-              hash[tag_stack.last].concat(data) if data
-            end
-          when XMLParser::PI
-          end
-        end
-      rescue XMLParserError
-        line = parser.line
-        column = parser.column
-        print "Parse error at #{line}(#{column}) : #{$!}\n"
-      end
-    end
-
-
-    def xmlparser_parse_program(tag, hash)
-      case tag
-      when 'BlastOutput_program'
-        @program = hash[tag]
-      when 'BlastOutput_version'
-        @version = hash[tag]
-      when 'BlastOutput_reference'
-        @reference = hash[tag]
-      when 'BlastOutput_db'
-        @db = hash[tag].strip
-      when 'BlastOutput_query-ID'
-        @query_id = hash[tag]
-      when 'BlastOutput_query-def'
-        @query_def = hash[tag]
-      when 'BlastOutput_query-len'
-        @query_len = hash[tag].to_i
-      end
-    end
-
-    # set parameter of the key as val
-    def xml_set_parameter(key, val)
-      #labels = { 
-      #  'matrix'       => 'Parameters_matrix',
-      #  'expect'       => 'Parameters_expect',
-      #  'include'      => 'Parameters_include',
-      #  'sc-match'     => 'Parameters_sc-match',
-      #  'sc-mismatch'  => 'Parameters_sc-mismatch',
-      #  'gap-open'     => 'Parameters_gap-open',
-      #  'gap-extend'   => 'Parameters_gap-extend',
-      #  'filter'       => 'Parameters_filter',
-      #  'pattern'      => 'Parameters_pattern',
-      #  'entrez-query' => 'Parameters_entrez-query',
-      #}
-      k = key.sub(/\AParameters\_/, '')
-      @parameters[k] =
-        case k
-        when 'expect', 'include'
-          val.to_f
-        when /\Agap\-/, /\Asc\-/
-          val.to_i
-        else
-          val
-        end
-    end
-
-    def xmlparser_parse_parameters(hash)
-      hash.each do |k, v|
-        xml_set_parameter(k, v)
-      end
-    end
-
-    def xmlparser_parse_iteration(tag, hash)
-      case tag
-      when 'Iteration_iter-num'
-        @iterations.last.num = hash[tag].to_i
-      when 'Iteration_message'
-        @iterations.last.message = hash[tag].to_s
-
-        # for new BLAST XML format
-      when 'Iteration_query-ID'
-        @iterations.last.query_id = hash[tag].to_s
-      when 'Iteration_query-def'
-        @iterations.last.query_def = hash[tag].to_s
-      when 'Iteration_query-len'
-        @iterations.last.query_len = hash[tag].to_i
-      end
-    end
-
-    def xmlparser_parse_hit(tag, hash)
-      hit = @iterations.last.hits.last
-      case tag
-      when 'Hit_num'
-        hit.num = hash[tag].to_i
-      when 'Hit_id'
-        hit.hit_id = hash[tag].clone
-      when 'Hit_def'
-        hit.definition = hash[tag].clone
-      when 'Hit_accession'
-        hit.accession = hash[tag].clone
-      when 'Hit_len'
-        hit.len = hash[tag].clone.to_i
-      end
-    end
-
-    def xmlparser_parse_hsp(hash)
-      hsp = @iterations.last.hits.last.hsps.last
-      hsp.num          = hash['Hsp_num'].to_i
-      hsp.bit_score    = hash['Hsp_bit-score'].to_f
-      hsp.score        = hash['Hsp_score'].to_i
-      hsp.evalue       = hash['Hsp_evalue'].to_f
-      hsp.query_from   = hash['Hsp_query-from'].to_i
-      hsp.query_to     = hash['Hsp_query-to'].to_i
-      hsp.hit_from     = hash['Hsp_hit-from'].to_i
-      hsp.hit_to       = hash['Hsp_hit-to'].to_i
-      hsp.pattern_from = hash['Hsp_pattern-from'].to_i
-      hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
-      hsp.query_frame  = hash['Hsp_query-frame'].to_i
-      hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
-      hsp.identity     = hash['Hsp_identity'].to_i
-      hsp.positive     = hash['Hsp_positive'].to_i
-      hsp.gaps         = hash['Hsp_gaps'].to_i
-      hsp.align_len    = hash['Hsp_align-len'].to_i
-      hsp.density      = hash['Hsp_density'].to_i
-      hsp.qseq         = hash['Hsp_qseq']
-      hsp.hseq         = hash['Hsp_hseq']
-      hsp.midline      = hash['Hsp_midline']
-    end
-
-    def xmlparser_parse_statistics(hash)
-      labels = {
-        'db-num'	=> 'Statistics_db-num',
-        'db-len'	=> 'Statistics_db-len',
-        'hsp-len'	=> 'Statistics_hsp-len',
-        'eff-space'	=> 'Statistics_eff-space',
-        'kappa'	=> 'Statistics_kappa',
-        'lambda'	=> 'Statistics_lambda',
-        'entropy'	=> 'Statistics_entropy'
-      }
-      labels.each do |k,v|
-        case k
-        when 'db-num', 'db-len', 'hsp-len'
-          @iterations.last.statistics[k] = hash[v].to_i
-        else
-          @iterations.last.statistics[k] = hash[v].to_f
-        end
-      end
-    end
-        
-  end # class Report
-end # class Blast
-end # module Bio
-
-
-=begin
-
-This file is automatically loaded by bio/appl/blast/report.rb
-
-=end