class Bio::LazyBlast::Report
Attributes
db[R]
program[R]
query_def[R]
query_id[R]
query_len[R]
statistics[R]
version[R]
Public Class Methods
new(filename)
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# File lib/bio/appl/blast/lazyblastxml.rb, line 9 def initialize(filename) @filename = filename @reader = LibXML::XML::Reader.file(@filename) @nodes = Enumerator.new do |yielder| while @reader.read yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT end end setup_report_values end
Public Instance Methods
each() { |iteration| ... }
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# File lib/bio/appl/blast/lazyblastxml.rb, line 51 def each @nodes.each{|node| yield Iteration.new(node) if node.name == "Iteration"} end
Also aliased as: each_iteration
rewind()
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# File lib/bio/appl/blast/lazyblastxml.rb, line 56 def rewind @reader.close @reader = LibXML::XML::Reader.file(@filename) @nodes = Enumerator.new do |yielder| while @reader.read yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT end end end
setup_report_values()
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# File lib/bio/appl/blast/lazyblastxml.rb, line 20 def setup_report_values @statistics = Hash.new @nodes.each do |node| return if node.name == "BlastOutput_iterations" case node.name when 'BlastOutput_program' @program = node.read_inner_xml when 'BlastOutput_version' @version = node.read_inner_xml when 'BlastOutput_db' @db = node.read_inner_xml when 'BlastOutput_query-ID' @query_id = node.read_inner_xml when 'BlastOutput_query-def' @query_def = node.read_inner_xml when 'BlastOutput_query-len' @query_len = node.read_inner_xml.to_i when 'Parameters_matrix' @statistics['matrix'] = node.read_inner_xml when 'Parameters_expect' @statistics['expect'] = node.read_inner_xml.to_i when 'Parameters_gap-open' @statistics['gap-open'] = node.read_inner_xml.to_i when 'Parameters_gap-extend' @statistics['gap-extend'] = node.read_inner_xml.to_i when 'Parameters_filter' @statistics['filter'] = node.read_inner_xml end end end