class Bio::LazyBlast::Report::Iteration::Hit::Hsp
Attributes
align_len[R]
bit_score[R]
density[R]
evalue[R]
gaps[R]
hit_frame[R]
hit_from[R]
hit_to[R]
hseq[R]
identity[R]
midline[R]
mismatch_count[R]
num[R]
percent_identity[R]
positive[R]
qseq[R]
query_frame[R]
query_from[R]
query_to[R]
Public Class Methods
new(reader)
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# File lib/bio/appl/blast/lazyblastxml.rb, line 141 def initialize(reader) @nodes = Enumerator.new do |yielder| until (reader.name == "Hsp" and reader.node_type == LibXML::XML::Reader::TYPE_END_ELEMENT) or !reader.read yielder << reader if reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT end end setup_hsp_values end
Public Instance Methods
setup_hsp_values()
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# File lib/bio/appl/blast/lazyblastxml.rb, line 150 def setup_hsp_values @nodes.each do |node| case node.name when 'Hsp_num' @num = node.read_inner_xml.to_i when 'Hsp_bit-score' @bit_score = node.read_inner_xml.to_f when 'Hsp_evalue' @evalue = node.read_inner_xml.to_f when 'Hsp_query-from' @query_from = node.read_inner_xml.to_i when 'Hsp_query-to' @query_to = node.read_inner_xml.to_i when 'Hsp_query-frame' @query_frame = node.read_inner_xml.to_i when 'Hsp_hit-frame' @hit_frame = node.read_inner_xml.to_i when 'Hsp_identity' @identity = node.read_inner_xml.to_i when 'Hsp_positive' @positive = node.read_inner_xml.to_i when 'Hsp_align-len' @align_len = node.read_inner_xml.to_i when 'Hsp_qseq' @qseq = node.read_inner_xml when 'Hsp_hseq' @hseq = node.read_inner_xml when 'Hsp_midline' @midline = node.read_inner_xml end end end